Compare commits
7 Commits
cc0a7d446d
...
bc228735a4
| Author | SHA1 | Date | |
|---|---|---|---|
|
bc228735a4 | ||
|
|
30b7175702 | ||
|
|
35d275c104 | ||
|
|
78156a8c95 | ||
|
|
0eae496a94 | ||
|
|
d49592c5d4 | ||
|
|
1d0db893f1 |
7
.gitignore
vendored
7
.gitignore
vendored
@@ -4,5 +4,10 @@
|
|||||||
/jupyterhub_volumes/jupyterhub
|
/jupyterhub_volumes/jupyterhub
|
||||||
/jupyterhub_volumes/caddy
|
/jupyterhub_volumes/caddy
|
||||||
/**/.DS_Store
|
/**/.DS_Store
|
||||||
|
/web_src/**/*.RData
|
||||||
|
/web_src/**/*.pdf
|
||||||
|
/web_src/**/*_files
|
||||||
|
/web_src/**/*_cache
|
||||||
/.luarc.json
|
/.luarc.json
|
||||||
|
/sandbox
|
||||||
|
*.log
|
||||||
|
|||||||
1
.vscode/ltex.hiddenFalsePositives.en-US.txt
vendored
Normal file
1
.vscode/ltex.hiddenFalsePositives.en-US.txt
vendored
Normal file
@@ -0,0 +1 @@
|
|||||||
|
{"rule":"MORFOLOGIK_RULE_EN_US","sentence":"^\\QA password that secures access to the system\nA user number or UID (User IDentifier) that identifies the user on the machine\nA location on the hard disk to store the user's files, called Home or home\nA group of users, which allows working in groups on the machine (see later)\\E$"}
|
||||||
862
fish-primers.qmd
Normal file
862
fish-primers.qmd
Normal file
@@ -0,0 +1,862 @@
|
|||||||
|
---
|
||||||
|
title: "Designing Fish primers"
|
||||||
|
format: revealjs
|
||||||
|
editor: visual
|
||||||
|
---
|
||||||
|
|
||||||
|
```{r setup, include=FALSE}
|
||||||
|
library(knitr)
|
||||||
|
```
|
||||||
|
|
||||||
|
# Preparing the data
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## What do we need ?
|
||||||
|
|
||||||
|
To design a new animal DNA metabarcode we download from the NCBI the following data
|
||||||
|
|
||||||
|
- The complete set of whole mitochondrial genomes
|
||||||
|
- The NCBI taxonomy
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## We need also:
|
||||||
|
|
||||||
|
- a Unix computer: a Mac or a Linux box
|
||||||
|
- A unix terminal window for typing commands
|
||||||
|
- Installed on the computer
|
||||||
|
- The OBITools --- <http://github.com/metabarcoding/obitools4>
|
||||||
|
- ecoPrimers --- <http://metabarcoding.org/ecoprimers>
|
||||||
|
- R --- <http://wwww.r-project.org>
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Downloading the mitochondrial genomes
|
||||||
|
|
||||||
|
We can use an internet browser and download the files from NCBI FTP website
|
||||||
|
|
||||||
|
{fig-align="center"}
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Downloading the mitochondrial genomes
|
||||||
|
|
||||||
|
We can use an internet browser and download the files from NCBI FTP website
|
||||||
|
|
||||||
|
or run the following command lines
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
curl 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/mitochondrion/mitochondrion.1.genomic.gbff.gz' \
|
||||||
|
> mito.all.gb.gz
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
zless mito.all.gb.gz
|
||||||
|
```
|
||||||
|
|
||||||
|
```
|
||||||
|
LOCUS NW_009243181 45189 bp DNA linear CON 06-OCT-2014
|
||||||
|
DEFINITION Fonticula alba strain ATCC 38817 mitochondrial scaffold
|
||||||
|
supercont2.211, whole genome shotgun sequence.
|
||||||
|
ACCESSION NW_009243181 NZ_AROH01000000
|
||||||
|
VERSION NW_009243181.1
|
||||||
|
DBLINK BioProject: PRJNA262900
|
||||||
|
Assembly: GCF_000388065.1
|
||||||
|
KEYWORDS WGS; RefSeq.
|
||||||
|
SOURCE mitochondrion Fonticula alba
|
||||||
|
ORGANISM Fonticula alba
|
||||||
|
Eukaryota; Rotosphaerida; Fonticulaceae; Fonticula.
|
||||||
|
REFERENCE 1 (bases 1 to 45189)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Downloading the complete taxonomy
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obitaxonomy --download-ncbi
|
||||||
|
```
|
||||||
|
|
||||||
|
```
|
||||||
|
INFO[0000] Number of workers set 16
|
||||||
|
INFO[0000] Downloading NCBI Taxdump to ncbitaxo_20250211.tgz
|
||||||
|
downloading 100% ████████████████████████████████████████| (66/66 MB, 5.1 MB/s)
|
||||||
|
```
|
||||||
|
|
||||||
|
The NCBI taxonomy contains all the relationship between taxa. Each taxon is identified by a unique numerical id: `taxid`
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## The archive contains several files
|
||||||
|
|
||||||
|
file: `nodes.dmp`
|
||||||
|
|
||||||
|
```
|
||||||
|
1 | 1 | no rank | | 8 | 0 | ...
|
||||||
|
2 | 131567 | superkingdom | | 0 | 0 |
|
||||||
|
6 | 335928 | genus | | 0 | 1 |
|
||||||
|
7 | 6 | species | AC | 0 | 1 |
|
||||||
|
9 | 32199 | species | BA | 0 |
|
||||||
|
10 | 135621 | genus | | 0 |
|
||||||
|
11 | 1707 | species | CG | 0 | 1 |
|
||||||
|
13 | 203488 | genus | | 0 | 1 |
|
||||||
|
14 | 13 | species | DT | 0 | 1 |
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## file: `names.dmp`
|
||||||
|
|
||||||
|
```
|
||||||
|
1 | root | | scientific name |
|
||||||
|
2 | Bacteria | Bacteria <prokaryote> | scientific name |
|
||||||
|
2 | Monera | Monera <Bacteria> | in-part |
|
||||||
|
2 | Procaryotae | Procaryotae <Bacteria> | in-part |
|
||||||
|
2 | Prokaryota | Prokaryota <Bacteria> | in-part |
|
||||||
|
2 | Prokaryotae | Prokaryotae <Bacteria> | in-part |
|
||||||
|
2 | bacteria | bacteria <blast2> | blast name |
|
||||||
|
2 | eubacteria | | genbank common name |
|
||||||
|
2 | prokaryote | prokaryote <Bacteria> | in-part |
|
||||||
|
...
|
||||||
|
10 | Cellvibrio | | scientific name |
|
||||||
|
11 | [Cellvibrio] gilvus | | scientific name |
|
||||||
|
13 | Dictyoglomus | | scientific name |
|
||||||
|
14 | Dictyoglomus thermophilum | | scientific name |
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Preparing the set of complete genomes
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obiconvert --skip-empty \
|
||||||
|
--update-taxid \
|
||||||
|
-t ncbitaxo_20250211.tgz \
|
||||||
|
mito.all.gb.gz \
|
||||||
|
> mito.all.fasta
|
||||||
|
head -5 mito.all.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
five first lines of the new `mito.all.fasta` file
|
||||||
|
|
||||||
|
```
|
||||||
|
>NC_072933 {"definition":"Echinosophora koreensis mitochondrion, complete genome.","scientific_name":"mitochondrion Echinosophora koreensis","taxid":228658}
|
||||||
|
ctttcgggtcggaaatagaagatctggattagatcccttctcgatagctttagtcagagc
|
||||||
|
tcatccctcgaaaaagggagtagtgagatgagaaaagggtgactagaatacggaaattca
|
||||||
|
actagtgaagtcagatccgggaattccactattgaagttatccgtcttaggcttcaagca
|
||||||
|
agctatctttcaaggaagtcagtctaagccctaagccaagatctgctttttgccagtcaa
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## We want:
|
||||||
|
|
||||||
|
- annotate sequences by their species `taxid`
|
||||||
|
- keep a single genome per species
|
||||||
|
- extract only vertebrate genome
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Looking for the **Vertebrata**'s taxid
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obitaxonomy -t ncbitaxo_20250211.tgz \
|
||||||
|
--fixed \
|
||||||
|
'vertebrata'
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
taxid,parent,taxonomic_rank,scientific_name
|
||||||
|
taxon:1261581 [Vertebrata]@genus,taxon:2008651 [Polysiphonioideae]@subfamily,genus,Vertebrata
|
||||||
|
taxon:7742 [Vertebrata]@clade,taxon:89593 [Craniata]@subphylum,clade,Vertebrata
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Looking for the **Vertebrata**'s taxid
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obitaxonomy -t ncbitaxo_20250211.tgz \
|
||||||
|
--fixed \
|
||||||
|
'vertebrata' \
|
||||||
|
| csvlook
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
| taxid | parent | taxonomic_rank | scientific_name |
|
||||||
|
| -------------------------------- | ------------------------------------------- | -------------- | --------------- |
|
||||||
|
| taxon:1261581 [Vertebrata]@genus | taxon:2008651 [Polysiphonioideae]@subfamily | genus | Vertebrata |
|
||||||
|
| taxon:7742 [Vertebrata]@clade | taxon:89593 [Craniata]@subphylum | clade | Vertebrata |
|
||||||
|
```
|
||||||
|
|
||||||
|
## A genus called **Vertebrata**
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obitaxonomy -t ncbitaxo_20250211.tgz \
|
||||||
|
-p 2008651 \
|
||||||
|
| csvlook
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
| taxid | parent | taxonomic_rank | scientific_name |
|
||||||
|
| ------------------------------------------- | ------------------------------------------- | -------------- | ------------------ |
|
||||||
|
| taxon:2008651 [Polysiphonioideae]@subfamily | taxon:2803 [Rhodomelaceae]@family | subfamily | Polysiphonioideae |
|
||||||
|
| taxon:2803 [Rhodomelaceae]@family | taxon:2802 [Ceramiales]@order | family | Rhodomelaceae |
|
||||||
|
| taxon:2802 [Ceramiales]@order | taxon:2045261 [Rhodymeniophycidae]@subclass | order | Ceramiales |
|
||||||
|
| taxon:2045261 [Rhodymeniophycidae]@subclass | taxon:2806 [Florideophyceae]@class | subclass | Rhodymeniophycidae |
|
||||||
|
| taxon:2806 [Florideophyceae]@class | taxon:2763 [Rhodophyta]@phylum | class | Florideophyceae |
|
||||||
|
| taxon:2763 [Rhodophyta]@phylum | taxon:2759 [Eukaryota]@superkingdom | phylum | Rhodophyta |
|
||||||
|
| taxon:2759 [Eukaryota]@superkingdom | taxon:131567 [cellular organisms]@no rank | superkingdom | Eukaryota |
|
||||||
|
| taxon:131567 [cellular organisms]@no rank | taxon:1 [root]@no rank | no rank | cellular organisms |
|
||||||
|
| taxon:1 [root]@no rank | taxon:1 [root]@no rank | no rank | root |
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Reannotation and selection of the genomes
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obiannotate -t ncbitaxo_20250211.tgz \
|
||||||
|
--with-taxon-at-rank=species \
|
||||||
|
mito.all.fasta | \
|
||||||
|
obiannotate -S 'ori_taxid=annotations.taxid' | \
|
||||||
|
obiannotate -S 'taxid=annotations.species_taxid' | \
|
||||||
|
obiuniq -c taxid > mito.one.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Species representation
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
|
||||||
|
obicsv -k taxid mito.one.fasta \
|
||||||
|
| tail -n +2 \
|
||||||
|
| sort \
|
||||||
|
| uniq -c \
|
||||||
|
| sort -nk1 \
|
||||||
|
| cut -w -f 2 \
|
||||||
|
| uplot count
|
||||||
|
```
|
||||||
|
|
||||||
|
```
|
||||||
|
┌ ┐
|
||||||
|
1 ┤■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 17769.0
|
||||||
|
2 ┤ 90.0
|
||||||
|
3 ┤ 17.0
|
||||||
|
4 ┤ 5.0
|
||||||
|
5 ┤ 4.0
|
||||||
|
6 ┤ 2.0
|
||||||
|
7 ┤ 1.0
|
||||||
|
└ ┘
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Selection of the vertebrata genomes
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
|
||||||
|
obigrep -t ncbitaxo_20250211.tgz \
|
||||||
|
-r 7742 \
|
||||||
|
mito.one.fasta > mito.vert.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
|
||||||
|
obicount mito.vert.fasta \
|
||||||
|
| csvlook
|
||||||
|
```
|
||||||
|
|
||||||
|
```
|
||||||
|
| entities | n |
|
||||||
|
| -------- | ----------- |
|
||||||
|
| variants | 7,822 |
|
||||||
|
| reads | 7,823 |
|
||||||
|
| symbols | 131,378,756 |
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Prepare data for ecoPrimers 1/3
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
mkdir ncbitaxo_20250211
|
||||||
|
cd ncbitaxo_20250211
|
||||||
|
tar zxvf ../ncbitaxo_20250211.tgz
|
||||||
|
cd ..
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Prepare data for ecoPrimers 2/3
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obiconvert -O mito.vert.fasta > mito.vert.old.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
head -5 mito.vert.old.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
>NC_071784 taxid=taxon:2065826 [Sineleotris saccharae]@species; count=1; ori_taxid=taxon:2065826 [Sineleotris saccharae]@species; scientific_name=mitochondrion Sineleotris saccharae; species_name=Sineleotris saccharae; species_taxid=taxon:2065826 [Sineleotris saccharae]@species; Sineleotris saccharae mitochondrion, complete genome.
|
||||||
|
gctagcgtagcttaaccaaagcataacactgaagatgttaagatgggccctagaaagccc
|
||||||
|
cgcaagcacaaaagcttggtcctggctttactatcagcttaggctaaacttacacatgca
|
||||||
|
agtatccgcatccccgtgagaatgcccttaagctcccaccgctaacaggagtcaaggagc
|
||||||
|
cggtatcaggcacaaccctgagttagcccacgacaccttgctcagccacacccccaaggg
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Prepare data for ecoPrimers 3/3
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
ecoPCRFormat -t ncbitaxo_20250211 \
|
||||||
|
-f \
|
||||||
|
-n vertebrata \
|
||||||
|
mito.vert.old.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
ls -l vertebrata*
|
||||||
|
```
|
||||||
|
|
||||||
|
```
|
||||||
|
-rw-r--r--@ 1 coissac staff 260899785 Feb 11 11:53 vertabrata.ndx
|
||||||
|
-rw-r--r--@ 1 coissac staff 546 Feb 11 11:53 vertabrata.rdx
|
||||||
|
-rw-r--r--@ 1 coissac staff 121379751 Feb 11 11:53 vertabrata.tdx
|
||||||
|
-rw-r--r--@ 1 coissac staff 40446318 Feb 11 11:54 vertabrata_001.sdx
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Looking for the *Teleostei* `taxid`
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obitaxonomy -t ncbitaxo_20250211.tgz \
|
||||||
|
--fixed \
|
||||||
|
'Teleostei' \
|
||||||
|
| csvlook
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
| taxid | parent | taxonomic_rank | scientific_name |
|
||||||
|
| ---------------------------------- | ---------------------------------- | -------------- | --------------- |
|
||||||
|
| taxon:32443 [Teleostei]@infraclass | taxon:41665 [Neopterygii]@subclass | infraclass | Teleostei |
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Selecting the best primer pairs
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
ecoPrimers -d vertebrata \
|
||||||
|
-e 3 -3 2 \
|
||||||
|
-l 30 -L 150 \
|
||||||
|
-r 32443 \
|
||||||
|
-c > Teleostei.ecoprimers
|
||||||
|
```
|
||||||
|
|
||||||
|
- Total pair count : 9407
|
||||||
|
- Total good pair count : 407
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
head -35 Teleostei.ecoprimers
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
#
|
||||||
|
# ecoPrimer version 0.5
|
||||||
|
# Rank level optimisation : species
|
||||||
|
# max error count by oligonucleotide : 3
|
||||||
|
#
|
||||||
|
# Restricted to taxon:
|
||||||
|
# 32443 : Teleostei (infraclass)
|
||||||
|
#
|
||||||
|
# strict primer quorum : 0.70
|
||||||
|
# example quorum : 0.90
|
||||||
|
# counterexample quorum : 0.10
|
||||||
|
#
|
||||||
|
# database : vertebrata
|
||||||
|
# Database is constituted of 3909 examples corresponding to 3876 species
|
||||||
|
# and 0 counterexamples corresponding to 0 species
|
||||||
|
#
|
||||||
|
# amplifiat length between [30,150] bp
|
||||||
|
# DB sequences are considered as circular
|
||||||
|
# Pairs having specificity less than 0.60 will be ignored
|
||||||
|
#
|
||||||
|
0 AGAGTGACGGGCGGTGTG CGTCAGGTCGAGGTGTAG 62.8 42.4 57.5 34.1 12 11 GG 3864 0 0.988 3832 0 0.989 2731 0.713 134 146 138.22
|
||||||
|
1 CGTCAGGTCGAGGTGTAG GAGTGACGGGCGGTGTGT 57.5 34.1 63.1 42.9 11 12 GG 3863 0 0.988 3831 0 0.988 2730 0.713 133 145 137.22
|
||||||
|
2 CGTCAGGTCGAGGTGTAG GGGAGAGTGACGGGCGGT 57.5 34.1 64.5 37.0 11 13 GG 3811 0 0.975 3779 0 0.975 2689 0.712 137 149 141.22
|
||||||
|
3 CGTCAGGTCGAGGTGTAG GGGGAGAGTGACGGGCGG 57.5 34.1 65.5 38.4 11 14 GG 3804 0 0.973 3772 0 0.973 2682 0.711 138 149 142.22
|
||||||
|
4 ACACCGCCCGTCACTCTC ACCTTCCGGTACACTTAC 62.5 36.8 54.0 16.6 12 9 GG 3850 0 0.985 3818 0 0.985 2658 0.696 46 132 66.51
|
||||||
|
5 AACGTCAGGTCGAGGTGT AGAGTGACGGGCGGTGTG 58.8 28.4 62.8 41.7 10 12 GG 3779 0 0.967 3746 0 0.966 2653 0.708 137 148 140.23
|
||||||
|
6 ACACCGCCCGTCACTCTC CACCTTCCGGTACACTTA 62.5 36.8 54.0 16.6 12 9 GG 3846 0 0.984 3814 0 0.984 2654 0.696 47 133 67.51
|
||||||
|
7 AACGTCAGGTCGAGGTGT GAGTGACGGGCGGTGTGT 58.8 28.4 63.1 42.1 10 12 GG 3778 0 0.966 3745 0 0.966 2652 0.708 136 147 139.23
|
||||||
|
8 ACCTTCCGGTACACTTAC CACACCGCCCGTCACTCT 54.0 16.6 62.8 37.3 9 12 GG 3845 0 0.984 3813 0 0.984 2653 0.696 47 133 67.51
|
||||||
|
9 ACACCGCCCGTCACTCTC TCCGGTACACTTACCATG 62.5 36.8 54.1 18.1 12 9 GG 3851 0 0.985 3819 0 0.985 2651 0.694 42 128 62.51
|
||||||
|
10 ACACCGCCCGTCACTCTC CCGGTACACTTACCATGT 62.5 36.8 54.4 18.6 12 9 GG 3851 0 0.985 3819 0 0.985 2651 0.694 41 127 61.51
|
||||||
|
11 ACACCGCCCGTCACTCTC CCAAGTGCACCTTCCGGT 62.5 36.8 60.7 28.9 12 11 GG 3837 0 0.982 3805 0 0.982 2650 0.696 54 140 74.51
|
||||||
|
12 ACACCGCCCGTCACTCTC GCACCTTCCGGTACACTT 62.5 36.8 57.7 22.5 12 10 GG 3842 0 0.983 3810 0 0.983 2650 0.696 48 134 68.51
|
||||||
|
13 ACACCGCCCGTCACTCTC CGGTACACTTACCATGTT 62.5 36.8 52.4 15.7 12 8 GG 3850 0 0.985 3818 0 0.985 2650 0.694 40 126 60.51
|
||||||
|
14 ACACCGCCCGTCACTCTC CACTTACCATGTTACGAC 62.5 36.8 51.1 27.7 12 8 GG 3850 0 0.985 3817 0 0.985 2649 0.694 35 121 55.51
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
- Primer ID : 11
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
| Primer | sequence | tm max | tm min | GC count |
|
||||||
|
|---------|--------------------|--------|--------|----------|
|
||||||
|
| Forward | ACACCGCCCGTCACTCTC | 62.5 | 36.8 | 12 |
|
||||||
|
| Reverse | CCAAGTGCACCTTCCGGT | 60.7 | 28.9 | 11 |
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
- amplifying 3837/3909 sequences\
|
||||||
|
- identify 2650/3876 Species
|
||||||
|
- Size ranging from 54bp to 140bp (mean: 74.75 bp)
|
||||||
|
|
||||||
|
## Testing the new primer pair
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obipcr --forward ACACCGCCCGTCACTCTC \
|
||||||
|
--reverse CCAAGTGCACCTTCCGGT \
|
||||||
|
-e 5 \
|
||||||
|
-l 30 -L 150 \
|
||||||
|
-c \
|
||||||
|
mito.vert.fasta \
|
||||||
|
> Teleostei_11.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
head Teleostei_11.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
>NC_022183_sub[925..998] {"count":1,"definition":"Acrossocheilus hemispinus mitochondrion, complete genome.","direction":"forward","forward_error":1,"forward_match":"acaccgcccgtcaccctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:356810 [Acrossocheilus hemispinus]@species","reverse_error":0,"reverse_match":"ccaagtgcaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Acrossocheilus hemispinus","species_name":"Acrossocheilus hemispinus","species_taxid":"taxon:356810 [Acrossocheilus hemispinus]@species","taxid":"taxon:356810 [Acrossocheilus hemispinus]@species"}
|
||||||
|
cccgtcaaaatacaccaaaaatacttaatacaataacactaacaaggggaggcaagtcgt
|
||||||
|
aacatggtaagtgt
|
||||||
|
>NC_018560_sub[916..988] {"count":1,"definition":"Astatotilapia calliptera mitochondrion, complete genome.","direction":"forward","forward_error":0,"forward_match":"acaccgcccgtcactctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:8154 [Astatotilapia calliptera]@species","reverse_error":1,"reverse_match":"ccaagtacaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Astatotilapia calliptera (eastern happy)","species_name":"Astatotilapia calliptera","species_taxid":"taxon:8154 [Astatotilapia calliptera]@species","taxid":"taxon:8154 [Astatotilapia calliptera]@species"}
|
||||||
|
cccaagccaacaacatcctataaataatacattttaccggtaaaggggaggcaagtcgta
|
||||||
|
acatggtaagtgt
|
||||||
|
>NC_056117_sub[923..997] {"count":1,"definition":"Pseudocrossocheilus tridentis mitochondrion, complete genome.","direction":"forward","forward_error":0,"forward_match":"acaccgcccgtcactctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species","reverse_error":0,"reverse_match":"ccaagtgcaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Pseudocrossocheilus tridentis","species_name":"Pseudocrossocheilus tridentis","species_taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species","taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species"}
|
||||||
|
ccctgtcaaaaagcatcaaatatatataataaattagcaatgacaaggggaggcaagtcg
|
||||||
|
taacacggtaagtgt
|
||||||
|
>NC_045904_sub[919..997] {"count":1,"definition":"Eospalax fontanierii mitochondrion, complete genome.","direction":"forward","forward_error":1,"forward_match":"acaccgcccgtcgctctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:146134 [Eospalax fontanierii]@species","reverse_error":4,"reverse_match":"ccaagcacactttccagt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Eospalax fontanierii","species_name":"Eospalax fontanierii","species_taxid":"taxon:146134 [Eospalax fontanierii]@species","taxid":"taxon:146134 [Eospalax fontanierii]@species"}
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
convert the fasta file to csv
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obicsv --auto -s -i Teleostei_11.fasta > Teleostei_11.csv
|
||||||
|
```
|
||||||
|
|
||||||
|
and display the begining of the table
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
head Teleostei_11.csv | csvlook
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
| id | count | direction | forward_error | forward_match | forward_primer | ori_taxid | reverse_error | reverse_match | reverse_primer | scientific_name | species_name | species_taxid | taxid | sequence |
|
||||||
|
| ------------------------- | ----- | --------- | ------------- | ------------------ | ------------------ | ---------------------------------------------------- | ------------- | ------------------ | ------------------ | ------------------------------------------------------ | ----------------------------- | ---------------------------------------------------- | ---------------------------------------------------- | ------------------------------------------------------------------------------- |
|
||||||
|
| NC_022183_sub[925..998] | True | forward | True | acaccgcccgtcaccctc | ACACCGCCCGTCACTCTC | taxon:356810 [Acrossocheilus hemispinus]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Acrossocheilus hemispinus | Acrossocheilus hemispinus | taxon:356810 [Acrossocheilus hemispinus]@species | taxon:356810 [Acrossocheilus hemispinus]@species | cccgtcaaaatacaccaaaaatacttaatacaataacactaacaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_018560_sub[916..988] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:8154 [Astatotilapia calliptera]@species | 1 | ccaagtacaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Astatotilapia calliptera (eastern happy) | Astatotilapia calliptera | taxon:8154 [Astatotilapia calliptera]@species | taxon:8154 [Astatotilapia calliptera]@species | cccaagccaacaacatcctataaataatacattttaccggtaaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_056117_sub[923..997] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:887881 [Pseudocrossocheilus tridentis]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Pseudocrossocheilus tridentis | Pseudocrossocheilus tridentis | taxon:887881 [Pseudocrossocheilus tridentis]@species | taxon:887881 [Pseudocrossocheilus tridentis]@species | ccctgtcaaaaagcatcaaatatatataataaattagcaatgacaaggggaggcaagtcgtaacacggtaagtgt |
|
||||||
|
| NC_045904_sub[919..997] | True | forward | True | acaccgcccgtcgctctc | ACACCGCCCGTCACTCTC | taxon:146134 [Eospalax fontanierii]@species | 4 | ccaagcacactttccagt | CCAAGTGCACCTTCCGGT | mitochondrion Eospalax fontanierii | Eospalax fontanierii | taxon:146134 [Eospalax fontanierii]@species | taxon:146134 [Eospalax fontanierii]@species | ctcaagtacataaacttggatatattcttaataacccaacaaaaatattagaggagataagtcgtaacaaggtaagcat |
|
||||||
|
| NC_018546_sub[916..987] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:30732 [Oryzias melastigma]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Oryzias melastigma (Indian medaka) | Oryzias melastigma | taxon:30732 [Oryzias melastigma]@species | taxon:30732 [Oryzias melastigma]@species | cccgacccattttaaaaattaaataaaagatttcaggaactaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_044151_sub[922..993] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:2597641 [Sicyopterus squamosissimus]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Sicyopterus squamosissimus (cling goby) | Sicyopterus squamosissimus | taxon:2597641 [Sicyopterus squamosissimus]@species | taxon:2597641 [Sicyopterus squamosissimus]@species | cccaaaacaaacacacacataaataagaaaaaatgaaaataaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_044152_sub[922..994] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:2597642 [Sicyopterus stiphodonoides]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Sicyopterus stiphodonoides (cling goby) | Sicyopterus stiphodonoides | taxon:2597642 [Sicyopterus stiphodonoides]@species | taxon:2597642 [Sicyopterus stiphodonoides]@species | cccaaaacaaacacacacataaataagaaaaaantgaaaataaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_026976_sub[1453..1531] | True | forward | True | acaccgcccgtcactccc | ACACCGCCCGTCACTCTC | taxon:9545 [Macaca nemestrina]@species | 1 | ccaagtgcaccttccagt | CCAAGTGCACCTTCCGGT | mitochondrion Macaca nemestrina (pig-tailed macaque) | Macaca nemestrina | taxon:9545 [Macaca nemestrina]@species | taxon:9545 [Macaca nemestrina]@species | ctcaaatatatttaaggaacatcttaactaaacgccctaatatttatatagaggggataagtcgtaacatggtaagtgt |
|
||||||
|
| NC_031553_sub[921..995] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:643337 [Puntioplites proctozystron]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Puntioplites proctozystron | Puntioplites proctozystron | taxon:643337 [Puntioplites proctozystron]@species | taxon:643337 [Puntioplites proctozystron]@species | ccctgtcaaaacgcactaaaaatatctaatacaaaagcaccgacaaggggaggcaagtcgtaacacggtaagtgt |
|
||||||
|
```
|
||||||
|
|
||||||
|
# We are now switching to R
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Preparing our R session
|
||||||
|
|
||||||
|
First we have to download the two follong libraries
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
library(tidyverse)
|
||||||
|
library(ggpubr)
|
||||||
|
library(ROBITools4)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Loading the data
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
|
||||||
|
fish <- read_csv('Teleostei_11.csv', show_col_types = FALSE)
|
||||||
|
taxo <- read_ncbi_taxdump('ncbitaxo_20250211')
|
||||||
|
assign_default_taxonomy(taxo)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
Looking for Teleostei taxid
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
teleo_taxid <- ecofind('Teleostei')
|
||||||
|
teleo_taxid
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Format taxids
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
fish %>% mutate(
|
||||||
|
taxid = as_taxid(
|
||||||
|
as.integer(
|
||||||
|
str_split_fixed(
|
||||||
|
str_split_fixed(
|
||||||
|
taxid,pattern = " ",
|
||||||
|
n = 2)[,1],
|
||||||
|
":",
|
||||||
|
2)[,2]))
|
||||||
|
) %>%
|
||||||
|
as_tbl_obipcr() %>%
|
||||||
|
mutate(across(taxon(),
|
||||||
|
.names="category",
|
||||||
|
.fn=taxonomy_classifier(Teleostei = 32443))) %>%
|
||||||
|
group_by(category) %>%
|
||||||
|
mutate(weight = taxonomic_weights(taxid,taxo)) %>%
|
||||||
|
ungroup() -> fish
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## The fish tibble
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
head(fish,n = 4)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Identifying which sequences belongs fish
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
table(fish$category)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Testing the conservation of the priming sites
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward <- pssm(fish$forward_match,
|
||||||
|
weights = fish$weight,
|
||||||
|
categories = fish$category)
|
||||||
|
|
||||||
|
pssm_reverse <- pssm(fish$reverse_match,
|
||||||
|
weights = fish$weight,
|
||||||
|
categories = fish$category)
|
||||||
|
```
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Rescaling the matrix as Shanon entropy
|
||||||
|
|
||||||
|
$$
|
||||||
|
H = - \sum_{i \in \{A,C,G,T\}} p_i \times \frac{\log(p_i)}{\log(2)}
|
||||||
|
$$
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward <- pssm_scale_shanon(pssm_forward)
|
||||||
|
pssm_reverse <- pssm_scale_shanon(pssm_reverse)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Display the rescaled matrix
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## The DNA logo of our primer pair
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
flogo <- ggbarcodelogo(pssm_forward) +
|
||||||
|
xlab("Forward primer") + ylab("Bits")
|
||||||
|
rlogo <- ggbarcodelogo(pssm_reverse) +
|
||||||
|
xlab("Reverse primer") + ylab("Bits")
|
||||||
|
|
||||||
|
ggarrange(flogo,rlogo,ncol=2) -> dnaplot
|
||||||
|
|
||||||
|
dnaplot
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## How many mismatches ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
ggbarcodemistmatch(fish$forward_error,
|
||||||
|
fish$reverse_error,
|
||||||
|
otu=fish$species_name,
|
||||||
|
categories=fish$category) + theme_minimal()
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Are we discriminate taxa ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
with(fish %>% filter(category == "Teleostei"),
|
||||||
|
discriminated_at_rank(taxid,
|
||||||
|
c("species","genus","family","order"),
|
||||||
|
sequence))
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## How many sequences will provide information at rank ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
with(fish %>% filter(category == "Teleostei"),
|
||||||
|
discriminant_at_rank(taxid,
|
||||||
|
c("species","genus","family","order"),
|
||||||
|
sequence))
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Is it the same for *Cyprinidae* ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
cyprinidae_taxid <- ecofind('Cyprinidae')
|
||||||
|
cyprinidae_taxid
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Classify according to both categories
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
fish %>%
|
||||||
|
mutate(across(taxon(),
|
||||||
|
.names="category2",
|
||||||
|
.fn=taxonomy_classifier(Teleostei = 32443,
|
||||||
|
Cyprinidae = 7953))) -> fish
|
||||||
|
|
||||||
|
table(fish$category2)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Are we discriminate taxa ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
with(fish %>% filter(category2 == "Cyprinidae"),
|
||||||
|
discriminated_at_rank(taxid,
|
||||||
|
c("species","genus"),
|
||||||
|
sequence))
|
||||||
|
```
|
||||||
|
|
||||||
|
# Go back to unix
|
||||||
|
|
||||||
|
## We run ecoPrimers and ecoPCR on the select primer pair
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
ecoPrimers -d vertebrata \
|
||||||
|
-e 3 -3 2 \
|
||||||
|
-l 30 -L 150 \
|
||||||
|
-r 7953 -c > Cyprinidae.ecoprimers
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obipcr --forward ACGGCGTAAAGGGTGGTT \
|
||||||
|
--reverse TATCTAATCCCAGTTTGT \
|
||||||
|
-e 5 \
|
||||||
|
-l 30 -L 500 \
|
||||||
|
-c \
|
||||||
|
mito.vert.fasta \
|
||||||
|
> Cyprinidae_14.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obicsv --auto -s -i Cyprinidae_14.fasta > Cyprinidae_14.csv
|
||||||
|
```
|
||||||
|
|
||||||
|
# Go back to R
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
cyprinidae <- read_csv('Cyprinidae_14.csv',
|
||||||
|
show_col_types = FALSE) %>%
|
||||||
|
mutate(
|
||||||
|
taxid = as_taxid(
|
||||||
|
as.integer(
|
||||||
|
str_split_fixed(
|
||||||
|
str_split_fixed(
|
||||||
|
taxid,pattern = " ",
|
||||||
|
n = 2)[,1],
|
||||||
|
":",
|
||||||
|
2)[,2]))
|
||||||
|
) %>%
|
||||||
|
as_tbl_obipcr() %>%
|
||||||
|
mutate(across(taxon(),
|
||||||
|
.names="category",
|
||||||
|
.fn=taxonomy_classifier(Teleostei = 32443,
|
||||||
|
Cyprinidae = 7953))) %>%
|
||||||
|
group_by(category) %>%
|
||||||
|
mutate(weight = taxonomic_weights(taxid,taxo)) %>%
|
||||||
|
ungroup()
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Identifying which sequences belongs fish and *Cyprinidae*
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
table(cyprinidae$category)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Looking for conservation
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward <- pssm(cyprinidae$forward_match,
|
||||||
|
weights = cyprinidae$weight,
|
||||||
|
categories = cyprinidae$category) %>%
|
||||||
|
pssm_scale_shanon()
|
||||||
|
|
||||||
|
pssm_reverse <- pssm(cyprinidae$reverse_match,
|
||||||
|
weights = cyprinidae$weight,
|
||||||
|
categories = cyprinidae$category) %>%
|
||||||
|
pssm_scale_shanon()
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Plot the new DNA logo
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
flogo <- ggbarcodelogo(pssm_forward) +
|
||||||
|
xlab("Forward primer") + ylab("Bits")
|
||||||
|
rlogo <- ggbarcodelogo(pssm_reverse) +
|
||||||
|
xlab("Reverse primer") + ylab("Bits")
|
||||||
|
|
||||||
|
ggarrange(flogo,rlogo,ncol=2) -> dnaplot
|
||||||
|
|
||||||
|
dnaplot
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## How many mismatches ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
ggbarcodemistmatch(cyprinidae$forward_error,
|
||||||
|
cyprinidae$reverse_error,
|
||||||
|
otu=cyprinidae$species_name,
|
||||||
|
categories=cyprinidae$category) + theme_minimal()
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Are we discriminate *Cyprinidae* taxa ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
with(cyprinidae %>% filter(category == "Cyprinidae"),
|
||||||
|
discriminated_at_rank(taxid,
|
||||||
|
c("species","genus"),
|
||||||
|
sequence))
|
||||||
|
```
|
||||||
1227
jupyterhub_volumes/course/biodiversity_metrics_exercises.ipynb
Normal file
1227
jupyterhub_volumes/course/biodiversity_metrics_exercises.ipynb
Normal file
File diff suppressed because it is too large
Load Diff
1559
jupyterhub_volumes/course/unix_exercises_bash.ipynb
Normal file
1559
jupyterhub_volumes/course/unix_exercises_bash.ipynb
Normal file
File diff suppressed because it is too large
Load Diff
Binary file not shown.
|
Before Width: | Height: | Size: 217 KiB After Width: | Height: | Size: 350 KiB |
@@ -115,6 +115,7 @@
|
|||||||
<nav>
|
<nav>
|
||||||
<ul id="nav-menu"></ul>
|
<ul id="nav-menu"></ul>
|
||||||
<ul class="admin-links">
|
<ul class="admin-links">
|
||||||
|
<li><a href="/obidoc/" target="_blank">OBITools 4 Doc</a></li>
|
||||||
<li><a href="/jupyter/" target="_blank">JupyterHub</a></li>
|
<li><a href="/jupyter/" target="_blank">JupyterHub</a></li>
|
||||||
<li><a href="/sftp/" target="_blank">Data Admin</a></li>
|
<li><a href="/sftp/" target="_blank">Data Admin</a></li>
|
||||||
</ul>
|
</ul>
|
||||||
|
|||||||
56
jupyterhub_volumes/web/obidoc/404.html
Normal file
56
jupyterhub_volumes/web/obidoc/404.html
Normal file
@@ -0,0 +1,56 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="en">
|
||||||
|
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||||
|
<meta name="description" content="">
|
||||||
|
<meta name="theme-color" media="(prefers-color-scheme: light)" content="#ffffff">
|
||||||
|
<meta name="theme-color" media="(prefers-color-scheme: dark)" content="#343a40">
|
||||||
|
<meta name="color-scheme" content="light dark"><meta property="og:url" content="http://metabar:8888/obidoc/404.html">
|
||||||
|
<meta property="og:site_name" content="OBITools4 documentation">
|
||||||
|
<meta property="og:title" content="404 Page not found">
|
||||||
|
<meta property="og:locale" content="en_us">
|
||||||
|
<meta property="og:type" content="website">
|
||||||
|
<title>404 Page not found | OBITools4 documentation</title>
|
||||||
|
<link rel="icon" href="/obidoc/favicon.png" >
|
||||||
|
<link rel="manifest" href="/obidoc/manifest.json">
|
||||||
|
<link rel="canonical" href="http://metabar:8888/obidoc/404.html">
|
||||||
|
<link rel="stylesheet" href="/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css" integrity="sha256-X9e44tHArhXaJ5xS/zJzETA4b3G1jwEUaPINAFb+a3g=" crossorigin="anonymous">
|
||||||
|
<script defer src="/obidoc/fuse.min.js"></script>
|
||||||
|
<script defer src="/obidoc/en.search.min.4da51bdd2d833922fdbc0e19df517221387fc625ffb68ee140d605b3c5b68058.js" integrity="sha256-TaUb3S2DOSL9vA4Z31FyITh/xiX/to7hQNYFs8W2gFg=" crossorigin="anonymous"></script>
|
||||||
|
|
||||||
|
<script defer src="/obidoc/sw.min.32af8eafce4180aa1c5dea66d99fb26ba9043ea7c7a4c706138c91d9051b285e.js" integrity="sha256-Mq+Or85BgKocXepm2Z+ya6kEPqfHpMcGE4yR2QUbKF4=" crossorigin="anonymous"></script>
|
||||||
|
<!--
|
||||||
|
Made with Book Theme
|
||||||
|
https://github.com/alex-shpak/hugo-book
|
||||||
|
-->
|
||||||
|
<link rel="stylesheet" type="text/css" href="http://metabar:8888/obidoc/hugo-cite.css" />
|
||||||
|
|
||||||
|
<style>
|
||||||
|
.not-found {
|
||||||
|
text-align: center;
|
||||||
|
}
|
||||||
|
.not-found h1 {
|
||||||
|
margin: .25em 0 0 0;
|
||||||
|
opacity: .25;
|
||||||
|
font-size: 40vmin;
|
||||||
|
}
|
||||||
|
</style>
|
||||||
|
</head>
|
||||||
|
|
||||||
|
<body>
|
||||||
|
<main class="flex justify-center not-found">
|
||||||
|
<div>
|
||||||
|
<h1>404</h1>
|
||||||
|
<h2>Page Not Found</h2>
|
||||||
|
<h3>
|
||||||
|
<a href="/obidoc/">OBITools4 documentation</a>
|
||||||
|
</h3>
|
||||||
|
</div>
|
||||||
|
</main>
|
||||||
|
|
||||||
|
|
||||||
|
</body>
|
||||||
|
|
||||||
|
</html>
|
||||||
File diff suppressed because one or more lines are too long
1590
jupyterhub_volumes/web/obidoc/categories/index.html
Normal file
1590
jupyterhub_volumes/web/obidoc/categories/index.html
Normal file
File diff suppressed because it is too large
Load Diff
11
jupyterhub_volumes/web/obidoc/categories/index.xml
Normal file
11
jupyterhub_volumes/web/obidoc/categories/index.xml
Normal file
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Categories on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/categories/</link>
|
||||||
|
<description>Recent content in Categories on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/categories/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
@@ -0,0 +1,9 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="en-us">
|
||||||
|
<head>
|
||||||
|
<title>http://metabar:8888/obidoc/categories/</title>
|
||||||
|
<link rel="canonical" href="http://metabar:8888/obidoc/categories/">
|
||||||
|
<meta charset="utf-8">
|
||||||
|
<meta http-equiv="refresh" content="0; url=http://metabar:8888/obidoc/categories/">
|
||||||
|
</head>
|
||||||
|
</html>
|
||||||
1590
jupyterhub_volumes/web/obidoc/commands/index.html
Normal file
1590
jupyterhub_volumes/web/obidoc/commands/index.html
Normal file
File diff suppressed because it is too large
Load Diff
11
jupyterhub_volumes/web/obidoc/commands/index.xml
Normal file
11
jupyterhub_volumes/web/obidoc/commands/index.xml
Normal file
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Commands on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/commands/</link>
|
||||||
|
<description>Recent content in Commands on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/commands/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
9
jupyterhub_volumes/web/obidoc/commands/page/1/index.html
Normal file
9
jupyterhub_volumes/web/obidoc/commands/page/1/index.html
Normal file
@@ -0,0 +1,9 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="en-us">
|
||||||
|
<head>
|
||||||
|
<title>http://metabar:8888/obidoc/commands/</title>
|
||||||
|
<link rel="canonical" href="http://metabar:8888/obidoc/commands/">
|
||||||
|
<meta charset="utf-8">
|
||||||
|
<meta http-equiv="refresh" content="0; url=http://metabar:8888/obidoc/commands/">
|
||||||
|
</head>
|
||||||
|
</html>
|
||||||
@@ -0,0 +1 @@
|
|||||||
|
.admonition{margin:1rem 0;border-radius:4px;box-shadow:0 1px 3px rgba(0,0,0,0.12);transition:all 0.3s ease}.admonition-header{padding:0.5rem 1rem;display:flex;align-items:center;font-weight:600;border-bottom:1px solid rgba(0,0,0,0.1);font-size:1.1rem;border-radius:4px 4px 0 0}.admonition-header svg{width:1.1em;height:1.1em;margin-right:0.5rem;fill:currentColor}.admonition-content{padding:1rem;background-color:#fff;border-radius:0 0 4px 4px;color:#000;transition:background-color 0.3s ease, color 0.3s ease}.admonition-content p{margin:0 0 0.5rem 0}.admonition-content p:last-child{margin-bottom:0}.admonition-content ul,.admonition-content ol{margin:0 0 0.5rem 0;padding-left:1.2rem}.admonition-content ul:last-child,.admonition-content ol:last-child{margin-bottom:0}.admonition-content blockquote{margin:0 0 0.5rem 0;padding-left:1rem;border-left:3px solid #e0e0e0}.admonition-content blockquote:last-child{margin-bottom:0}.admonition-content code{background-color:#f5f5f5;color:#24292e;padding:0.2em 0.4em;border-radius:3px;font-size:0.9em}@media (prefers-color-scheme: dark){.admonition-content{background-color:#1D1E20;color:#e6e6e6}.admonition-content code{background-color:#313244;color:#cdd6f4}.admonition-content blockquote{border-left-color:#45475a;color:#cdd6f4}}body.dark .admonition-content{background-color:#1D1E20;color:#e6e6e6}body.dark .admonition-content code{background-color:#313244;color:#cdd6f4}body.dark .admonition-content blockquote{border-left-color:#45475a;color:#cdd6f4}.admonition.abstract{background:transparent;border-left:4px solid #209fb5}.admonition.abstract .admonition-header{background:rgba(32,159,181,0.1);color:#209fb5}.admonition.caution{background:transparent;border-left:4px solid #e64553}.admonition.caution .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.code{background:transparent;border-left:4px solid #7287fd}.admonition.code .admonition-header{background:rgba(114,135,253,0.1);color:#7287fd}.admonition.conclusion{background:transparent;border-left:4px solid #dd7878}.admonition.conclusion .admonition-header{background:rgba(221,120,120,0.1);color:#dd7878}.admonition.danger{background:transparent;border-left:4px solid #fe640b}.admonition.danger .admonition-header{background:rgba(254,100,11,0.1);color:#fe640b}.admonition.error{background:transparent;border-left:4px solid #d20f39}.admonition.error .admonition-header{background:rgba(210,15,57,0.1);color:#d20f39}.admonition.example{background:transparent;border-left:4px solid #dc8a78}.admonition.example .admonition-header{background:rgba(220,138,120,0.1);color:#dc8a78}.admonition.experiment{background:transparent;border-left:4px solid #51bb2a}.admonition.experiment .admonition-header{background:rgba(81,187,42,0.1);color:#51bb2a}.admonition.goal{background:transparent;border-left:4px solid #e64553}.admonition.goal .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.idea{background:transparent;border-left:4px solid #df8e1d}.admonition.idea .admonition-header{background:rgba(223,142,29,0.1);color:#df8e1d}.admonition.important{background:transparent;border-left:4px solid #7D4DDA}.admonition.important .admonition-header{background:rgba(125,77,218,0.1);color:#7D4DDA}.admonition.info{background:transparent;border-left:4px solid #04a5e5}.admonition.info .admonition-header{background:rgba(4,165,229,0.1);color:#04a5e5}.admonition.memo{background:transparent;border-left:4px solid #e64553}.admonition.memo .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.note{background:transparent;border-left:4px solid #096ae1}.admonition.note .admonition-header{background:rgba(9,106,225,0.1);color:#096ae1}.admonition.notify{background:transparent;border-left:4px solid #0d48bd}.admonition.notify .admonition-header{background:rgba(13,72,189,0.1);color:#0d48bd}.admonition.question{background:transparent;border-left:4px solid #179299}.admonition.question .admonition-header{background:rgba(23,146,153,0.1);color:#179299}.admonition.quote{background:transparent;border-left:4px solid #7287fd}.admonition.quote .admonition-header{background:rgba(114,135,253,0.1);color:#7287fd}.admonition.success{background:transparent;border-left:4px solid #40a02b}.admonition.success .admonition-header{background:rgba(64,160,43,0.1);color:#40a02b}.admonition.task{background:transparent;border-left:4px solid #8839ef}.admonition.task .admonition-header{background:rgba(136,57,239,0.1);color:#8839ef}.admonition.tip{background:transparent;border-left:4px solid #179299}.admonition.tip .admonition-header{background:rgba(23,146,153,0.1);color:#179299}.admonition.warning{background:transparent;border-left:4px solid #df8e1d}.admonition.warning .admonition-header{background:rgba(223,142,29,0.1);color:#df8e1d}
|
||||||
1589
jupyterhub_volumes/web/obidoc/docs/about/index.html
Normal file
1589
jupyterhub_volumes/web/obidoc/docs/about/index.html
Normal file
File diff suppressed because it is too large
Load Diff
1530
jupyterhub_volumes/web/obidoc/docs/commands/advanced/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/commands/advanced/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Advanced tools on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/advanced/</link>
|
||||||
|
<description>Recent content in Advanced tools on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/advanced/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1530
jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Sequence alignments on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/alignments/</link>
|
||||||
|
<description>Recent content in Sequence alignments on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Exact alignment on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/exact-alignment/</link>
|
||||||
|
<description>Recent content in Exact alignment on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -0,0 +1,149 @@
|
|||||||
|
---
|
||||||
|
title: "Untitled"
|
||||||
|
format: html
|
||||||
|
editor: visual
|
||||||
|
---
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
library(tidyverse)
|
||||||
|
library(plotly)
|
||||||
|
library(matrixStats)
|
||||||
|
```
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
log_sum_exp <- function(a,b) {
|
||||||
|
m <- map2_dbl(a,b,max)
|
||||||
|
m + log(exp(a-m)+exp(b-m))
|
||||||
|
}
|
||||||
|
```
|
||||||
|
|
||||||
|
$$
|
||||||
|
\log(1 - e^b) = \log\left(-e^{(1-b)}\right)
|
||||||
|
$$
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
log1m_exp <- function(b) {
|
||||||
|
if (any(b >= 0)) {
|
||||||
|
stop(glue::glue("b must be negative (b={b})"))
|
||||||
|
}
|
||||||
|
return(log(-expm1(b))) # expm1(b) = exp(b) - 1, pour éviter les erreurs d'arrondi
|
||||||
|
}
|
||||||
|
```
|
||||||
|
|
||||||
|
$$
|
||||||
|
\log(e^a - e^b) = a + \log(1 - e^{b-a})
|
||||||
|
$$
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
log_diff_exp <- function(a, b) {
|
||||||
|
# Vérifier si a > b pour éviter des résultats indéfinis
|
||||||
|
if (any(a < b)) {
|
||||||
|
stop(glue::glue("Erreur : a ({a}) doit etre strictement sup<75>rieur <20> b ({b}) pour que e^a - e^b soit positif."))
|
||||||
|
}
|
||||||
|
|
||||||
|
# Calculer log(e^a - e^b) de manière stable
|
||||||
|
ifelse(a == b, -Inf,a + log1m_exp(b-a))
|
||||||
|
}
|
||||||
|
```
|
||||||
|
|
||||||
|
$$
|
||||||
|
P_{error} = 10^{-\frac{Q}{10}}
|
||||||
|
$$
|
||||||
|
|
||||||
|
$$
|
||||||
|
\begin{aligned}
|
||||||
|
q_F &= -\frac{Q_F}{10} \cdot \log(10) \\
|
||||||
|
q_R &= -\frac{Q_R}{10} \cdot \log(10) \\
|
||||||
|
P(macth | Obs(match)) &= (1-e^{q_F}) (1-e^{q_R}) + (1-e^{q_F})\frac{e^{q_R}}{4}+ (1-e^{q_R})\frac{e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||||
|
&=1 - e^{q_R} - e^{q_F} + e^{q_F+q_R} + \frac{e^{q_R}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||||
|
&= \frac{4 - 4e^{q_F} - 4e^{q_R} + 4e^{q_F+q_R} + e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4} \\
|
||||||
|
&= \frac{4 - 3e^{q_F}- 3e^{q_R} + 3e^{q_F+q_R}}{4}\\
|
||||||
|
&= \frac{4 - 3(e^{q_F}+e^{q_R}-e^{q_F+q_R})}{4} \\
|
||||||
|
&= 1 - \frac{3}{4}\left(e^{q_F}+e^{q_R}-e^{q_F+q_R}\right)
|
||||||
|
\end{aligned}
|
||||||
|
$$
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
Pm_match_observed <- function(Q_F, Q_R) {
|
||||||
|
l10 <- log(10)
|
||||||
|
l3 <- log(3)
|
||||||
|
l4 <- log(4)
|
||||||
|
|
||||||
|
q_F <- -Q_F/10*l10
|
||||||
|
q_R <- -Q_R/10*l10
|
||||||
|
|
||||||
|
term1 <- log_sum_exp(q_F,q_R)
|
||||||
|
term2 <- log_diff_exp(term1,q_F+q_R) + l3 - l4
|
||||||
|
|
||||||
|
log1m_exp(term2)
|
||||||
|
}
|
||||||
|
```
|
||||||
|
|
||||||
|
$$
|
||||||
|
\begin{aligned}
|
||||||
|
P(macth | Obs(mismatch)) &= \frac{(1-e^{q_F})e^{q_R}}{4} + \frac{(1-e^{q_R})e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||||
|
&= \frac{(1-e^{q_F})e^{q_R} + (1-e^{q_R})e^{q_F} + e^{q_F+q_R}}{4} \\
|
||||||
|
&= \frac{e^{q_R} - e^{q_F+q_R} + e^{q_F} - e^{q_F+q_R} + e^{q_F+q_R}}{4} \\
|
||||||
|
&= \frac{e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4}
|
||||||
|
\end{aligned}
|
||||||
|
$$
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
Pm_mismatch_observed <- function(Q_F, Q_R) {
|
||||||
|
l10 <- log(10)
|
||||||
|
l3 <- log(3)
|
||||||
|
l4 <- log(4)
|
||||||
|
|
||||||
|
q_F <- -Q_F/10*l10
|
||||||
|
q_R <- -Q_R/10*l10
|
||||||
|
|
||||||
|
term1 <- log_sum_exp(q_F,q_R)
|
||||||
|
log_diff_exp(term1,q_F+q_R) - l4
|
||||||
|
}
|
||||||
|
```
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
score_match_observed <- function(Q_F, Q_R) {
|
||||||
|
Pm_match_observed(Q_F,Q_R) - log1m_exp(Pm_match_observed(Q_F,Q_R))
|
||||||
|
}
|
||||||
|
|
||||||
|
score_mismatch_observed <- function(Q_F, Q_R) {
|
||||||
|
Pm_mismatch_observed(Q_F,Q_R) - log1m_exp(Pm_mismatch_observed(Q_F,Q_R))
|
||||||
|
}
|
||||||
|
```
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
scores <- expand_grid(QF=0:40,QR=0:40) %>%
|
||||||
|
mutate(score_match_observed = round(score_match_observed(QF,QR),2),
|
||||||
|
score_mismatch_observed = round(score_mismatch_observed(QF,QR),2))
|
||||||
|
```
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
plot_match <- plot_ly(scores,
|
||||||
|
x=~QF, y=~QR, z=~score_match_observed,
|
||||||
|
type="mesh3d") %>%
|
||||||
|
layout(
|
||||||
|
plot_bgcolor = "#bababa",
|
||||||
|
scene = list(
|
||||||
|
xaxis = list(title = "Q forward read"), # Change x/y/z axis title
|
||||||
|
yaxis = list(title = "Q reverse read"),
|
||||||
|
zaxis = list(title = "Score match")))
|
||||||
|
```
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
plot_mismatch <- plot_ly(scores,
|
||||||
|
x=~QF, y=~QR, z=~score_mismatch_observed,
|
||||||
|
type="mesh3d") %>%
|
||||||
|
layout(
|
||||||
|
plot_bgcolor = "#bababa",
|
||||||
|
scene = list(
|
||||||
|
xaxis = list(title = "Q forward read"), # Change x/y/z axis title
|
||||||
|
yaxis = list(title = "Q reverse read"),
|
||||||
|
zaxis = list(title = "Score mismatch")))
|
||||||
|
```
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
write(plotly_json(plot_match,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/match.json")
|
||||||
|
write(plotly_json(plot_mismatch,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/mismatch.json")
|
||||||
|
|
||||||
|
```
|
||||||
Binary file not shown.
|
After Width: | Height: | Size: 27 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>The FASTA-like alignment on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/</link>
|
||||||
|
<description>Recent content in The FASTA-like alignment on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1530
jupyterhub_volumes/web/obidoc/docs/commands/basics/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/commands/basics/index.html
Normal file
File diff suppressed because it is too large
Load Diff
12
jupyterhub_volumes/web/obidoc/docs/commands/basics/index.xml
Normal file
12
jupyterhub_volumes/web/obidoc/docs/commands/basics/index.xml
Normal file
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Basics on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/basics/</link>
|
||||||
|
<description>Recent content in Basics on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/basics/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Demultiplexing samples on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/demultiplexing/</link>
|
||||||
|
<description>Recent content in Demultiplexing samples on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/demultiplexing/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1530
jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Experimentals on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/experimental/</link>
|
||||||
|
<description>Recent content in Experimentals on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/experimental/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1530
jupyterhub_volumes/web/obidoc/docs/commands/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/commands/index.html
Normal file
File diff suppressed because it is too large
Load Diff
19
jupyterhub_volumes/web/obidoc/docs/commands/index.xml
Normal file
19
jupyterhub_volumes/web/obidoc/docs/commands/index.xml
Normal file
@@ -0,0 +1,19 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>The OBITools4 commands on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/</link>
|
||||||
|
<description>Recent content in The OBITools4 commands on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate>Fri, 04 Oct 2024 17:16:03 +0200</lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
<item>
|
||||||
|
<title>Glossary of tags</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/tags/</link>
|
||||||
|
<pubDate>Fri, 04 Oct 2024 17:16:03 +0200</pubDate>
|
||||||
|
<guid>http://metabar:8888/obidoc/docs/commands/tags/</guid>
|
||||||
|
<description><h1 id="glossary-of-tags">
 Glossary of tags
 <a class="anchor" href="#glossary-of-tags">#</a>
</h1>
<h3 id="--d--">
 - D -
 <a class="anchor" href="#--d--">#</a>
</h3>
<ul>
<li>
<p><strong>definition</strong> :</p>
<blockquote>
<p>text information about the sequence present in the original sequence file.</p>
</blockquote>
</li>
<li>
<p><strong>direction</strong> :</p>
<blockquote>
<p>set to “forward” if the original sequence did not need to be reverse-complemented to be processed, set to “reverse” otherwise.
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
</ul>
<h3 id="--f--">
 - F -
 <a class="anchor" href="#--f--">#</a>
</h3>
<ul>
<li>
<p><strong>forward_error</strong> :</p>
<blockquote>
<p>Number of mismatch between forward primer and priming site
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
<li>
<p><strong>forward_match</strong> :</p>
<blockquote>
<p>Forward primer priming site sequence
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
<li>
<p><strong>forward_primer</strong> :</p>
<blockquote>
<p>Forward primer sequence
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p></description>
|
||||||
|
</item>
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1753
jupyterhub_volumes/web/obidoc/docs/commands/options/index.html
Normal file
1753
jupyterhub_volumes/web/obidoc/docs/commands/options/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Shared command options on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/options/</link>
|
||||||
|
<description>Recent content in Shared command options on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/options/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
@@ -0,0 +1,6 @@
|
|||||||
|
>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
|
||||||
|
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
|
||||||
|
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
|
||||||
|
agcttaaaactcaaaggacctggcagttctttatatccct
|
||||||
1530
jupyterhub_volumes/web/obidoc/docs/commands/others/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/commands/others/index.html
Normal file
File diff suppressed because it is too large
Load Diff
12
jupyterhub_volumes/web/obidoc/docs/commands/others/index.xml
Normal file
12
jupyterhub_volumes/web/obidoc/docs/commands/others/index.xml
Normal file
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Others on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/others/</link>
|
||||||
|
<description>Recent content in Others on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/others/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1719
jupyterhub_volumes/web/obidoc/docs/commands/tags/index.html
Normal file
1719
jupyterhub_volumes/web/obidoc/docs/commands/tags/index.html
Normal file
File diff suppressed because it is too large
Load Diff
1530
jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Taxonomy on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/commands/taxonomy/</link>
|
||||||
|
<description>Recent content in Taxonomy on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/commands/taxonomy/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
@@ -0,0 +1,604 @@
|
|||||||
|
#!/usr/bin/env python3
|
||||||
|
|
||||||
|
import re
|
||||||
|
import gzip
|
||||||
|
import struct
|
||||||
|
import sys
|
||||||
|
import time
|
||||||
|
import getopt
|
||||||
|
from functools import cmp_to_key
|
||||||
|
|
||||||
|
_dbenable=False
|
||||||
|
|
||||||
|
#####
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Generic file function
|
||||||
|
#
|
||||||
|
#
|
||||||
|
#####
|
||||||
|
|
||||||
|
def universalOpen(file):
|
||||||
|
if isinstance(file,str):
|
||||||
|
if file[-3:] == '.gz':
|
||||||
|
rep = gzip.open(file)
|
||||||
|
else:
|
||||||
|
rep = open(file)
|
||||||
|
else:
|
||||||
|
rep = file
|
||||||
|
return rep
|
||||||
|
|
||||||
|
def universalTell(file):
|
||||||
|
if isinstance(file, gzip.GzipFile):
|
||||||
|
file=file.myfileobj
|
||||||
|
return file.tell()
|
||||||
|
|
||||||
|
def fileSize(file):
|
||||||
|
if isinstance(file, gzip.GzipFile):
|
||||||
|
file=file.myfileobj
|
||||||
|
pos = file.tell()
|
||||||
|
file.seek(0,2)
|
||||||
|
length = file.tell()
|
||||||
|
file.seek(pos,0)
|
||||||
|
return length
|
||||||
|
|
||||||
|
def progressBar(pos,max,reset=False,delta=[]):
|
||||||
|
if reset:
|
||||||
|
del delta[:]
|
||||||
|
if not delta:
|
||||||
|
delta.append(time.time())
|
||||||
|
delta.append(time.time())
|
||||||
|
|
||||||
|
delta[1]=time.time()
|
||||||
|
elapsed = delta[1]-delta[0]
|
||||||
|
percent = float(pos)/max * 100
|
||||||
|
remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent)))
|
||||||
|
bar = '#' * int(percent/2)
|
||||||
|
bar+= '|/-\\-'[pos % 5]
|
||||||
|
bar+= ' ' * (50 - int(percent/2))
|
||||||
|
sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain))
|
||||||
|
|
||||||
|
#####
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# NCBI Dump Taxonomy reader
|
||||||
|
#
|
||||||
|
#
|
||||||
|
#####
|
||||||
|
|
||||||
|
def endLessIterator(endedlist):
|
||||||
|
for x in endedlist:
|
||||||
|
yield x
|
||||||
|
while(1):
|
||||||
|
yield endedlist[-1]
|
||||||
|
|
||||||
|
class ColumnFile(object):
|
||||||
|
|
||||||
|
def __init__(self,stream,sep=None,strip=True,types=None):
|
||||||
|
if isinstance(stream,str):
|
||||||
|
self._stream = open(stream)
|
||||||
|
else:
|
||||||
|
try:
|
||||||
|
iter(stream)
|
||||||
|
self._stream = stream
|
||||||
|
except TypeError:
|
||||||
|
raise ValueError('stream must be string or an iterator')
|
||||||
|
self._delimiter=sep
|
||||||
|
self._strip=strip
|
||||||
|
if types:
|
||||||
|
self._types=[x for x in types]
|
||||||
|
for i in range(len(self._types)):
|
||||||
|
if self._types[i] is bool:
|
||||||
|
self._types[i]=ColumnFile.str2bool
|
||||||
|
else:
|
||||||
|
self._types=None
|
||||||
|
|
||||||
|
def str2bool(x):
|
||||||
|
return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
|
||||||
|
|
||||||
|
str2bool = staticmethod(str2bool)
|
||||||
|
|
||||||
|
|
||||||
|
def __iter__(self):
|
||||||
|
return self
|
||||||
|
|
||||||
|
def __next__(self):
|
||||||
|
ligne = next(self._stream)
|
||||||
|
data = ligne.split(self._delimiter)
|
||||||
|
if self._strip or self._types:
|
||||||
|
data = [x.strip() for x in data]
|
||||||
|
if self._types:
|
||||||
|
it = endLessIterator(self._types)
|
||||||
|
data = [x[1](x[0]) for x in ((y,next(it)) for y in data)]
|
||||||
|
return data
|
||||||
|
|
||||||
|
def taxonCmp(t1,t2):
|
||||||
|
if t1[0] < t2[0]:
|
||||||
|
return -1
|
||||||
|
elif t1[0] > t2[0]:
|
||||||
|
return +1
|
||||||
|
return 0
|
||||||
|
|
||||||
|
def bsearchTaxon(taxonomy,taxid):
|
||||||
|
taxCount = len(taxonomy)
|
||||||
|
begin = 0
|
||||||
|
end = taxCount
|
||||||
|
oldcheck=taxCount
|
||||||
|
check = int(begin + end / 2)
|
||||||
|
while check != oldcheck and taxonomy[check][0]!=taxid :
|
||||||
|
if taxonomy[check][0] < taxid:
|
||||||
|
begin=check
|
||||||
|
else:
|
||||||
|
end=check
|
||||||
|
oldcheck=check
|
||||||
|
check = int((begin + end) / 2)
|
||||||
|
|
||||||
|
|
||||||
|
if taxonomy[check][0]==taxid:
|
||||||
|
return check
|
||||||
|
else:
|
||||||
|
return None
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def readNodeTable(file):
|
||||||
|
|
||||||
|
file = universalOpen(file)
|
||||||
|
|
||||||
|
nodes = ColumnFile(file,
|
||||||
|
sep='|',
|
||||||
|
types=(int,int,str,
|
||||||
|
str,str,bool,
|
||||||
|
int,bool,int,
|
||||||
|
bool,bool,bool,str))
|
||||||
|
print("Reading taxonomy dump file...", file=sys.stderr)
|
||||||
|
taxonomy=[[n[0],n[2],n[1]] for n in nodes]
|
||||||
|
print("List all taxonomy rank...", file=sys.stderr)
|
||||||
|
ranks =list(set(x[1] for x in taxonomy))
|
||||||
|
ranks.sort()
|
||||||
|
ranks = {rank: index for index, rank in enumerate(ranks)}
|
||||||
|
|
||||||
|
print("Sorting taxons...", file=sys.stderr)
|
||||||
|
taxonomy.sort(key=lambda x: x[0])
|
||||||
|
|
||||||
|
print("Indexing taxonomy...", file=sys.stderr)
|
||||||
|
index = {}
|
||||||
|
for t in taxonomy:
|
||||||
|
index[t[0]]=bsearchTaxon(taxonomy, t[0])
|
||||||
|
|
||||||
|
print("Indexing parent and rank...", file=sys.stderr)
|
||||||
|
for t in taxonomy:
|
||||||
|
t[1]=ranks[t[1]]
|
||||||
|
t[2]=index[t[2]]
|
||||||
|
|
||||||
|
|
||||||
|
return taxonomy,ranks,index
|
||||||
|
|
||||||
|
def nameIterator(file):
|
||||||
|
file = universalOpen(file)
|
||||||
|
names = ColumnFile(file,
|
||||||
|
sep='|',
|
||||||
|
types=(int,str,
|
||||||
|
str,str))
|
||||||
|
for taxid,name,unique,classname,white in names:
|
||||||
|
yield taxid,name,classname
|
||||||
|
|
||||||
|
def mergedNodeIterator(file):
|
||||||
|
file = universalOpen(file)
|
||||||
|
merged = ColumnFile(file,
|
||||||
|
sep='|',
|
||||||
|
types=(int,int,str))
|
||||||
|
for taxid,current,white in merged:
|
||||||
|
yield taxid,current
|
||||||
|
|
||||||
|
def deletedNodeIterator(file):
|
||||||
|
file = universalOpen(file)
|
||||||
|
deleted = ColumnFile(file,
|
||||||
|
sep='|',
|
||||||
|
types=(int,str))
|
||||||
|
for taxid,white in deleted:
|
||||||
|
yield taxid
|
||||||
|
|
||||||
|
def readTaxonomyDump(taxdir):
|
||||||
|
taxonomy,ranks,index = readNodeTable('%s/nodes.dmp' % taxdir)
|
||||||
|
|
||||||
|
print("Adding scientific name...", file=sys.stderr)
|
||||||
|
|
||||||
|
alternativeName=[]
|
||||||
|
for taxid,name,classname in nameIterator('%s/names.dmp' % taxdir):
|
||||||
|
alternativeName.append((name,classname,index[taxid]))
|
||||||
|
if classname == 'scientific name':
|
||||||
|
taxonomy[index[taxid]].append(name)
|
||||||
|
|
||||||
|
print("Adding taxid alias...", file=sys.stderr)
|
||||||
|
for taxid,current in mergedNodeIterator('%s/merged.dmp' % taxdir):
|
||||||
|
index[taxid]=index[current]
|
||||||
|
|
||||||
|
print("Adding deleted taxid...", file=sys.stderr)
|
||||||
|
for taxid in deletedNodeIterator('%s/delnodes.dmp' % taxdir):
|
||||||
|
index[taxid]=None
|
||||||
|
|
||||||
|
return taxonomy,ranks,alternativeName,index
|
||||||
|
|
||||||
|
#####
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Genbank/EMBL sequence reader
|
||||||
|
#
|
||||||
|
#
|
||||||
|
#####
|
||||||
|
|
||||||
|
def entryIterator(file):
|
||||||
|
file = universalOpen(file)
|
||||||
|
rep =[]
|
||||||
|
ligne = file.readline()
|
||||||
|
while ligne:
|
||||||
|
rep.append(ligne)
|
||||||
|
if ligne == '//\n':
|
||||||
|
rep = ''.join(rep)
|
||||||
|
yield rep
|
||||||
|
rep = []
|
||||||
|
ligne = file.readline()
|
||||||
|
|
||||||
|
def fastaEntryIterator(file):
|
||||||
|
file = universalOpen(file)
|
||||||
|
rep =[]
|
||||||
|
ligne = file.readline()
|
||||||
|
while ligne:
|
||||||
|
if ligne[0] == '>' and rep:
|
||||||
|
rep = ''.join(rep)
|
||||||
|
yield rep
|
||||||
|
rep = []
|
||||||
|
rep.append(ligne)
|
||||||
|
ligne = file.readline()
|
||||||
|
|
||||||
|
if rep:
|
||||||
|
rep = ''.join(rep)
|
||||||
|
yield rep
|
||||||
|
|
||||||
|
_cleanSeq = re.compile('[ \n0-9]+')
|
||||||
|
|
||||||
|
def cleanSeq(seq):
|
||||||
|
return _cleanSeq.sub('',seq)
|
||||||
|
|
||||||
|
|
||||||
|
_gbParseID = re.compile('(?<=^LOCUS {7})[^ ]+(?= )',re.MULTILINE)
|
||||||
|
_gbParseDE = re.compile('(?<=^DEFINITION {2}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
|
||||||
|
_gbParseSQ = re.compile('(?<=^ORIGIN).+?(?=^//$)',re.MULTILINE+re.DOTALL)
|
||||||
|
_gbParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
|
||||||
|
|
||||||
|
def genbankEntryParser(entry):
|
||||||
|
Id = _gbParseID.findall(entry)[0]
|
||||||
|
De = ' '.join(_gbParseDE.findall(entry)[0].split())
|
||||||
|
Sq = cleanSeq(_gbParseSQ.findall(entry)[0].upper())
|
||||||
|
try:
|
||||||
|
Tx = int(_gbParseTX.findall(entry)[0])
|
||||||
|
except IndexError:
|
||||||
|
Tx = None
|
||||||
|
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
|
||||||
|
|
||||||
|
######################
|
||||||
|
|
||||||
|
_cleanDef = re.compile('[\nDE]')
|
||||||
|
|
||||||
|
def cleanDef(definition):
|
||||||
|
return _cleanDef.sub('',definition)
|
||||||
|
|
||||||
|
_emblParseID = re.compile('(?<=^ID {3})[^ ]+(?=;)',re.MULTILINE)
|
||||||
|
_emblParseDE = re.compile('(?<=^DE {3}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
|
||||||
|
_emblParseSQ = re.compile('(?<=^ ).+?(?=^//$)',re.MULTILINE+re.DOTALL)
|
||||||
|
_emblParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
|
||||||
|
|
||||||
|
def emblEntryParser(entry):
|
||||||
|
Id = _emblParseID.findall(entry)[0]
|
||||||
|
De = ' '.join(cleanDef(_emblParseDE.findall(entry)[0]).split())
|
||||||
|
Sq = cleanSeq(_emblParseSQ.findall(entry)[0].upper())
|
||||||
|
try:
|
||||||
|
Tx = int(_emblParseTX.findall(entry)[0])
|
||||||
|
except IndexError:
|
||||||
|
Tx = None
|
||||||
|
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
|
||||||
|
|
||||||
|
|
||||||
|
######################
|
||||||
|
|
||||||
|
_fastaSplit=re.compile(';\\W*')
|
||||||
|
|
||||||
|
def parseFasta(seq):
|
||||||
|
seq=seq.split('\n')
|
||||||
|
title = seq[0].strip()[1:].split(None,1)
|
||||||
|
id=title[0]
|
||||||
|
if len(title) == 2:
|
||||||
|
field = _fastaSplit.split(title[1])
|
||||||
|
else:
|
||||||
|
field=[]
|
||||||
|
info = dict(x.split('=',1) for x in field if '=' in x)
|
||||||
|
definition = ' '.join([x for x in field if '=' not in x])
|
||||||
|
seq=(''.join([x.strip() for x in seq[1:]])).upper()
|
||||||
|
return id,seq,definition,info
|
||||||
|
|
||||||
|
|
||||||
|
def fastaEntryParser(entry):
|
||||||
|
id,seq,definition,info = parseFasta(entry)
|
||||||
|
Tx = info.get('taxid',None)
|
||||||
|
if Tx is not None:
|
||||||
|
match = re.search(r'taxon:(\d+)', Tx)
|
||||||
|
if match:
|
||||||
|
Tx = match.group(1)
|
||||||
|
Tx=int(Tx)
|
||||||
|
return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
|
||||||
|
|
||||||
|
|
||||||
|
def sequenceIteratorFactory(entryParser,entryIterator):
|
||||||
|
def sequenceIterator(file):
|
||||||
|
for entry in entryIterator(file):
|
||||||
|
yield entryParser(entry)
|
||||||
|
return sequenceIterator
|
||||||
|
|
||||||
|
|
||||||
|
def taxonomyInfo(entry,connection):
|
||||||
|
taxid = entry['taxid']
|
||||||
|
curseur = connection.cursor()
|
||||||
|
curseur.execute("""
|
||||||
|
select taxid,species,genus,family,
|
||||||
|
taxonomy.scientificName(taxid) as sn,
|
||||||
|
taxonomy.scientificName(species) as species_sn,
|
||||||
|
taxonomy.scientificName(genus) as genus_sn,
|
||||||
|
taxonomy.scientificName(family) as family_sn
|
||||||
|
from
|
||||||
|
(
|
||||||
|
select alias as taxid,
|
||||||
|
taxonomy.getSpecies(alias) as species,
|
||||||
|
taxonomy.getGenus(alias) as genus,
|
||||||
|
taxonomy.getFamily(alias) as family
|
||||||
|
from taxonomy.aliases
|
||||||
|
where id=%d ) as tax
|
||||||
|
""" % taxid)
|
||||||
|
rep = curseur.fetchone()
|
||||||
|
entry['current_taxid']=rep[0]
|
||||||
|
entry['species']=rep[1]
|
||||||
|
entry['genus']=rep[2]
|
||||||
|
entry['family']=rep[3]
|
||||||
|
entry['scientific_name']=rep[4]
|
||||||
|
entry['species_sn']=rep[5]
|
||||||
|
entry['genus_sn']=rep[6]
|
||||||
|
entry['family_sn']=rep[7]
|
||||||
|
return entry
|
||||||
|
|
||||||
|
#####
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Binary writer
|
||||||
|
#
|
||||||
|
#
|
||||||
|
#####
|
||||||
|
|
||||||
|
def ecoSeqPacker(sq):
|
||||||
|
|
||||||
|
compactseq = gzip.zlib.compress(bytes(sq['sequence'],"ascii"),9)
|
||||||
|
cptseqlength = len(compactseq)
|
||||||
|
delength = len(sq['definition'])
|
||||||
|
|
||||||
|
totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength
|
||||||
|
|
||||||
|
packed = struct.pack('> I I 20s I I I %ds %ds' % (delength,cptseqlength),
|
||||||
|
totalSize,
|
||||||
|
sq['taxid'],
|
||||||
|
bytes(sq['id'],"ascii"),
|
||||||
|
delength,
|
||||||
|
len(sq['sequence']),
|
||||||
|
cptseqlength,
|
||||||
|
bytes(sq['definition'],"ascii"),
|
||||||
|
compactseq)
|
||||||
|
|
||||||
|
assert len(packed) == totalSize+4, "error in sequence packing"
|
||||||
|
|
||||||
|
return packed
|
||||||
|
|
||||||
|
def ecoTaxPacker(tx):
|
||||||
|
|
||||||
|
namelength = len(tx[3])
|
||||||
|
|
||||||
|
totalSize = 4 + 4 + 4 + 4 + namelength
|
||||||
|
|
||||||
|
packed = struct.pack('> I I I I I %ds' % namelength,
|
||||||
|
totalSize,
|
||||||
|
tx[0],
|
||||||
|
tx[1],
|
||||||
|
tx[2],
|
||||||
|
namelength,
|
||||||
|
bytes(tx[3],"ascii"))
|
||||||
|
|
||||||
|
return packed
|
||||||
|
|
||||||
|
def ecoRankPacker(rank):
|
||||||
|
|
||||||
|
namelength = len(rank)
|
||||||
|
|
||||||
|
packed = struct.pack('> I %ds' % namelength,
|
||||||
|
namelength,
|
||||||
|
bytes(rank, 'ascii'))
|
||||||
|
|
||||||
|
return packed
|
||||||
|
|
||||||
|
def ecoNamePacker(name):
|
||||||
|
|
||||||
|
namelength = len(name[0])
|
||||||
|
classlength= len(name[1])
|
||||||
|
totalSize = namelength + classlength + 4 + 4 + 4 + 4
|
||||||
|
|
||||||
|
packed = struct.pack('> I I I I I %ds %ds' % (namelength,classlength),
|
||||||
|
totalSize,
|
||||||
|
int(name[1]=='scientific name'),
|
||||||
|
namelength,
|
||||||
|
classlength,
|
||||||
|
name[2],
|
||||||
|
bytes(name[0], 'ascii'),
|
||||||
|
bytes(name[1], 'ascii'))
|
||||||
|
|
||||||
|
return packed
|
||||||
|
|
||||||
|
def ecoSeqWriter(file,input,taxindex,parser):
|
||||||
|
output = open(file,'wb')
|
||||||
|
input = universalOpen(input)
|
||||||
|
inputsize = fileSize(input)
|
||||||
|
entries = parser(input)
|
||||||
|
seqcount=0
|
||||||
|
skipped = []
|
||||||
|
|
||||||
|
output.write(struct.pack('> I',seqcount))
|
||||||
|
|
||||||
|
progressBar(1, inputsize,reset=True)
|
||||||
|
for entry in entries:
|
||||||
|
if entry['taxid'] is not None:
|
||||||
|
try:
|
||||||
|
entry['taxid']=taxindex[entry['taxid']]
|
||||||
|
except KeyError:
|
||||||
|
entry['taxid']=None
|
||||||
|
if entry['taxid'] is not None:
|
||||||
|
seqcount+=1
|
||||||
|
output.write(ecoSeqPacker(entry))
|
||||||
|
else:
|
||||||
|
skipped.append(entry['id'])
|
||||||
|
where = universalTell(input)
|
||||||
|
progressBar(where, inputsize)
|
||||||
|
print(" Readed sequences : %d " % seqcount, end=' ', file=sys.stderr)
|
||||||
|
else:
|
||||||
|
skipped.append(entry['id'])
|
||||||
|
|
||||||
|
print(file=sys.stderr)
|
||||||
|
output.seek(0,0)
|
||||||
|
output.write(struct.pack('> I',seqcount))
|
||||||
|
|
||||||
|
output.close()
|
||||||
|
return skipped
|
||||||
|
|
||||||
|
|
||||||
|
def ecoTaxWriter(file,taxonomy):
|
||||||
|
output = open(file,'wb')
|
||||||
|
output.write(struct.pack('> I',len(taxonomy)))
|
||||||
|
|
||||||
|
for tx in taxonomy:
|
||||||
|
output.write(ecoTaxPacker(tx))
|
||||||
|
|
||||||
|
output.close()
|
||||||
|
|
||||||
|
def ecoRankWriter(file,ranks):
|
||||||
|
output = open(file,'wb')
|
||||||
|
output.write(struct.pack('> I',len(ranks)))
|
||||||
|
|
||||||
|
rankNames = list(ranks.keys())
|
||||||
|
rankNames.sort()
|
||||||
|
|
||||||
|
for rank in rankNames:
|
||||||
|
output.write(ecoRankPacker(rank))
|
||||||
|
|
||||||
|
output.close()
|
||||||
|
|
||||||
|
def nameCmp(n1,n2):
|
||||||
|
name1=n1[0].upper()
|
||||||
|
name2=n2[0].upper()
|
||||||
|
if name1 < name2:
|
||||||
|
return -1
|
||||||
|
elif name1 > name2:
|
||||||
|
return 1
|
||||||
|
return 0
|
||||||
|
|
||||||
|
|
||||||
|
def ecoNameWriter(file,names):
|
||||||
|
output = open(file,'wb')
|
||||||
|
output.write(struct.pack('> I',len(names)))
|
||||||
|
|
||||||
|
names.sort(key=lambda x:x[0].upper())
|
||||||
|
|
||||||
|
for name in names:
|
||||||
|
output.write(ecoNamePacker(name))
|
||||||
|
|
||||||
|
output.close()
|
||||||
|
|
||||||
|
def ecoDBWriter(prefix,taxonomy,seqFileNames,parser):
|
||||||
|
|
||||||
|
ecoRankWriter('%s.rdx' % prefix, taxonomy[1])
|
||||||
|
ecoTaxWriter('%s.tdx' % prefix, taxonomy[0])
|
||||||
|
ecoNameWriter('%s.ndx' % prefix, taxonomy[2])
|
||||||
|
|
||||||
|
filecount = 0
|
||||||
|
for filename in seqFileNames:
|
||||||
|
filecount+=1
|
||||||
|
sk=ecoSeqWriter('%s_%03d.sdx' % (prefix,filecount),
|
||||||
|
filename,
|
||||||
|
taxonomy[3],
|
||||||
|
parser)
|
||||||
|
if sk:
|
||||||
|
print("Skipped entry :", file=sys.stderr)
|
||||||
|
print(sk, file=sys.stderr)
|
||||||
|
|
||||||
|
def ecoParseOptions(arguments):
|
||||||
|
opt = {
|
||||||
|
'prefix' : 'ecodb',
|
||||||
|
'taxdir' : 'taxdump',
|
||||||
|
'parser' : sequenceIteratorFactory(genbankEntryParser,
|
||||||
|
entryIterator)
|
||||||
|
}
|
||||||
|
|
||||||
|
o,filenames = getopt.getopt(arguments,
|
||||||
|
'ht:T:n:gfe',
|
||||||
|
['help',
|
||||||
|
'taxonomy=',
|
||||||
|
'taxonomy_db=',
|
||||||
|
'name=',
|
||||||
|
'genbank',
|
||||||
|
'fasta',
|
||||||
|
'embl'])
|
||||||
|
|
||||||
|
for name,value in o:
|
||||||
|
if name in ('-h','--help'):
|
||||||
|
printHelp()
|
||||||
|
exit()
|
||||||
|
elif name in ('-t','--taxonomy'):
|
||||||
|
opt['taxmod']='dump'
|
||||||
|
opt['taxdir']=value
|
||||||
|
elif name in ('-T','--taxonomy_db'):
|
||||||
|
opt['taxmod']='db'
|
||||||
|
opt['taxdb']=value
|
||||||
|
elif name in ('-n','--name'):
|
||||||
|
opt['prefix']=value
|
||||||
|
elif name in ('-g','--genbank'):
|
||||||
|
opt['parser']=sequenceIteratorFactory(genbankEntryParser,
|
||||||
|
entryIterator)
|
||||||
|
|
||||||
|
elif name in ('-f','--fasta'):
|
||||||
|
opt['parser']=sequenceIteratorFactory(fastaEntryParser,
|
||||||
|
fastaEntryIterator)
|
||||||
|
|
||||||
|
elif name in ('-e','--embl'):
|
||||||
|
opt['parser']=sequenceIteratorFactory(emblEntryParser,
|
||||||
|
entryIterator)
|
||||||
|
else:
|
||||||
|
raise ValueError('Unknown option %s' % name)
|
||||||
|
|
||||||
|
return opt,filenames
|
||||||
|
|
||||||
|
def printHelp():
|
||||||
|
print("-----------------------------------")
|
||||||
|
print(" ecoPCRFormat.py")
|
||||||
|
print("-----------------------------------")
|
||||||
|
print("ecoPCRFormat.py [option] <argument>")
|
||||||
|
print("-----------------------------------")
|
||||||
|
print("-e --embl :[E]mbl format")
|
||||||
|
print("-f --fasta :[F]asta format")
|
||||||
|
print("-g --genbank :[G]enbank format")
|
||||||
|
print("-h --help :[H]elp - print this help")
|
||||||
|
print("-n --name :[N]ame of the new database created")
|
||||||
|
print("-t --taxonomy :[T]axonomy - path to the taxonomy database")
|
||||||
|
print(" :bcp-like dump from GenBank taxonomy database.")
|
||||||
|
print("-----------------------------------")
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
|
||||||
|
opt,filenames = ecoParseOptions(sys.argv[1:])
|
||||||
|
|
||||||
|
taxonomy = readTaxonomyDump(opt['taxdir'])
|
||||||
|
|
||||||
|
ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
|
||||||
|
|
||||||
2606
jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.html
Normal file
2606
jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Designing new barcodes on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/cookbook/ecoprimers/</link>
|
||||||
|
<description>Recent content in Designing new barcodes on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/ecoprimers/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
Binary file not shown.
|
After Width: | Height: | Size: 168 KiB |
103
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
Normal file
103
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
Normal file
@@ -0,0 +1,103 @@
|
|||||||
|
SHELL := /bin/bash
|
||||||
|
FTPNCBI=ftp.ncbi.nlm.nih.gov
|
||||||
|
GBURL=https://$(FTPNCBI)/genbank
|
||||||
|
GBRELEASE_URL=$(GBURL)/GB_Release_Number
|
||||||
|
|
||||||
|
TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
|
||||||
|
|
||||||
|
GBRELEASE:=$(shell curl $(GBRELEASE_URL))
|
||||||
|
|
||||||
|
GBDIV_ALL:=$(shell curl -L ${GBURL} \
|
||||||
|
| grep -E 'gb.+\.seq\.gz' \
|
||||||
|
| sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
|
||||||
|
| sort \
|
||||||
|
| uniq)
|
||||||
|
|
||||||
|
GBDIV=bct inv mam phg pln pri rod vrl vrt
|
||||||
|
DIRECTORIES=fasta fasta_fgs
|
||||||
|
|
||||||
|
GBFILE_ALL:=$(shell curl -L ${GBURL} \
|
||||||
|
| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
|
||||||
|
| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
|
||||||
|
|
||||||
|
|
||||||
|
SUFFIXES += .d
|
||||||
|
NODEPS:=clean taxonomy
|
||||||
|
DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
|
||||||
|
|
||||||
|
ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
|
||||||
|
#Chances are, these files don't exist. GMake will create them and
|
||||||
|
#clean up automatically afterwards
|
||||||
|
-include $(DEPFILES)
|
||||||
|
endif
|
||||||
|
|
||||||
|
|
||||||
|
all: depends directories FORCE
|
||||||
|
@make downloads
|
||||||
|
|
||||||
|
downloads: taxonomy fasta_files
|
||||||
|
@echo Genbank Release number $(GBRELEASE)
|
||||||
|
@echo all divisions : $(GBDIV_ALL)
|
||||||
|
|
||||||
|
FORCE:
|
||||||
|
@sleep 1
|
||||||
|
|
||||||
|
.PHONY: all directories depends taxonomy fasta_files FORCE
|
||||||
|
|
||||||
|
depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
|
||||||
|
|
||||||
|
division: $(GBDIV)
|
||||||
|
|
||||||
|
taxonomy: directories Release_$(GBRELEASE)/taxonomy
|
||||||
|
|
||||||
|
directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp
|
||||||
|
|
||||||
|
Release_$(GBRELEASE):
|
||||||
|
@mkdir -p $@
|
||||||
|
@echo Create $@ directory
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
|
||||||
|
@mkdir -p $@
|
||||||
|
@echo Create $@ directory
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
|
||||||
|
@mkdir -p $@
|
||||||
|
@echo Create $@ directory
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
|
||||||
|
@mkdir -p $@
|
||||||
|
@echo Create $@ directory
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
|
||||||
|
@echo Create depends directory
|
||||||
|
@mkdir -p Release_$(GBRELEASE)/depends
|
||||||
|
@for f in ${GBFILE_ALL} ; do \
|
||||||
|
echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
|
||||||
|
echo -e "\t@echo Downloading file : $$f..." ; \
|
||||||
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
|
||||||
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
|
||||||
|
echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@" ; \
|
||||||
|
echo ; \
|
||||||
|
div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
|
||||||
|
fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||||
|
fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||||
|
fasta_files="$$fasta_files $$fasta" ; \
|
||||||
|
fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
|
||||||
|
echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
|
||||||
|
echo -e "\t@echo converting file : \$$< in fasta" ; \
|
||||||
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
|
||||||
|
echo -e "\t@obiconvert -Z --fasta-output --skip-empty \\" ; \
|
||||||
|
echo -e "\t Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
|
||||||
|
echo -e "\t && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@ \\" ; \
|
||||||
|
echo -e "\t && rm -f Release_$(GBRELEASE)/tmp/$$f \\" ; \
|
||||||
|
echo -e "\t || rm -f \$$@" ; \
|
||||||
|
echo -e "\t@echo conversion of $$@ done." ; \
|
||||||
|
echo ; \
|
||||||
|
done > $@ ; \
|
||||||
|
echo >> $@ ; \
|
||||||
|
echo "fasta_files: $$fasta_files" >> $@ ;
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/taxonomy:
|
||||||
|
mkdir -p $@
|
||||||
|
curl -iL $(TAXOURL) \
|
||||||
|
| tar -C $@ -zxf -
|
||||||
2812
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.html
Normal file
2812
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Analysing an Illumina data set on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/cookbook/illumina/</link>
|
||||||
|
<description>Recent content in Analysing an Illumina data set on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/illumina/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
Binary file not shown.
|
After Width: | Height: | Size: 16 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,26 @@
|
|||||||
|
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
|
||||||
|
tttt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||||
|
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,24 @@
|
|||||||
|
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||||
|
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
@@ -0,0 +1,329 @@
|
|||||||
|
>HELIUM_000100422_612GNAAXX:7:56:19300:10949#0/1_sub[28..127] {"count":37,"merged_sample":{"29a_F260619":37},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":43}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:63:4595:15643#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagtactaccggcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:7:8807:7823#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtcataccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:108:19171:11413#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:8:6794:4925#0/1_sub[28..127]":"(t)->(g)@38"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaagtagtcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:44:5008:2115#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:53:16956:10563#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||||
|
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:54:10323:7022#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
|
||||||
|
ttagccctaaacacaaataattatataaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:45:7460:13396#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatgcccgt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:58:8409:9911#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:100:18844:15930#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaagcgcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:29:9723:20435#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattgttcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:43:4660:16319#0/1_sub[28..126] {"count":22,"merged_sample":{"26a_F040644":22},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":42}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:103:11045:3860#0/1_sub[28..127] {"count":4,"merged_sample":{"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":4}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaagggcttggcggtgctttatgccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:67:10944:19430#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgtcagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacgtggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:56:6962:17278#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":7}}
|
||||||
|
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:60:13553:20530#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
atgttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:35:13167:18371#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccggagaactactaggaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:105:1895:7593#0/1_sub[28..127] {"count":11,"merged_sample":{"29a_F260619":11},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":13}}
|
||||||
|
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
|
||||||
|
agcttaaaactcaaaggacctggcggtgcttcatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:118:15661:12736#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattatccgcaagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:30:8391:13152#0/1_sub[28..127] {"count":17,"merged_sample":{"13a_F730603":17},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":25}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
||||||
|
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:95:14375:10838#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":5}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcagtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:82:13334:18499#0/1_sub[28..127] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":10}}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:108:11272:1128#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactactagcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:7:6016:14767#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacgtctagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:9:8337:12329#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":6}}
|
||||||
|
ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:15:12854:18952#0/1_sub[28..126] {"count":10,"merged_sample":{"29a_F260619":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":16}}
|
||||||
|
ttagccctaaacataagctattccataacaaaattattcgccagagtactaccggcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:1:4513:20277#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaaccattctataacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:57:18237:6765#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattatgcgccagagtactgccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:119:8691:15994#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcgat
|
||||||
|
agcttaaaacgcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:6:1739:11421#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgctagagtactactagcaaca
|
||||||
|
gcctgacactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:73:17136:17728#0/1_sub[28..127] {"count":6,"merged_sample":{"13a_F730603":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaattattcgccagagtactaccggcaac
|
||||||
|
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:76:9874:3117#0/1_sub[28..127] {"count":9,"merged_sample":{"29a_F260619":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:18:16679:15889#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||||
|
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:52:6908:8410#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":10}}
|
||||||
|
ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:71:13461:7411#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagaagactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
|
||||||
|
tttt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:47:6989:13864#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:72:8941:18482#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
|
||||||
|
gcctaaaactcaaaggacttggtggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:25:10818:13742#0/1_sub[28..133] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||||
|
ttagccctaaacgtaaactgcaaactattccataataaaataattcgcccaagaactact
|
||||||
|
agcaacagcttaaaactcaaaggacttggtggtgctttctacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:70:11509:6042#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||||
|
ttagccctaaacacaagaaattaatataacaaaaatattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:46:4342:17317#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||||
|
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgccttacgtccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:111:17844:17230#0/1_sub[28..126] {"count":13,"merged_sample":{"26a_F040644":13},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":17}}
|
||||||
|
ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gcttaaaactcaaaggacgtggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:34:17680:16952#0/1_sub[28..127] {"count":15,"merged_sample":{"13a_F730603":15},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":15}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgcttcacaccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:34:2640:2539#0/1_sub[28..127] {"count":19,"merged_sample":{"29a_F260619":19},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":25}}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:71:18891:9661#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gcttaaaactcaaaggacgtggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:26:16553:1613#0/1_sub[77..81] {"count":38,"merged_sample":{"13a_F730603":38},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":38}}
|
||||||
|
caata
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:45:5732:11220#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggtggtgctttctacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:1:14254:1103#0/1_sub[28..126] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:50:17151:20608#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||||
|
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:96:13203:2879#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":6}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
||||||
|
agcccaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:78:18041:18996#0/1_sub[28..126] {"count":13,"merged_sample":{"13a_F730603":9,"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s"},"obiclean_weight":{"13a_F730603":9,"15a_F730814":4}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:80:18387:10166#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:100:14685:15065#0/1_sub[28..127]":"(a)->(t)@24","HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127]":"(t)->(g)@71"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||||
|
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaacgcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:54:10113:12172#0/1_sub[28..127] {"count":7,"merged_sample":{"15a_F730814":4,"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":5,"29a_F260619":4}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:97:17822:18365#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatcccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:87:6328:12406#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcagtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:7:4611:13145#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacgtccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:78:6346:5817#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
|
||||||
|
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
|
||||||
|
agcccaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:7:15122:17310#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:94:6384:20392#0/1_sub[28..127]":"(a)->(t)@52"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacttcctgcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:27:7695:17738#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:48:15379:13773#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
|
||||||
|
ttagccctaaacatagataattttacaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:117:16246:17184#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":10}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:87:11044:6323#0/1_sub[28..126] {"count":69,"merged_sample":{"26a_F040644":69},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":84}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:40:12248:18615#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||||
|
ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:7:6470:13562#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacctccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:72:11850:15705#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:82:8566:4827#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":9}}
|
||||||
|
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
|
||||||
|
gcctaaaactcaaaggacttggtggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:43:16297:17399#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:7:15117:2564#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacctccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:90:4058:17862#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:43:13909:1377#0/1_sub[28..126] {"count":10,"merged_sample":{"26a_F040644":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":14}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
|
||||||
|
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:36:3584:21256#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaagctattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatgccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:80:13357:2959#0/1_sub[74..81] {"count":12,"merged_sample":{"29a_F260619":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
|
||||||
|
ccgatagg
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:70:8097:4516#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||||
|
ttagccctaaacataaacattcaagaaacaagaatgttcaccagagtactactagcaatg
|
||||||
|
gcctaaaactcaaaggacttggcagtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:7:8746:5790#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacctctagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:8:9165:18915#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactatgaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:85:7323:6139#0/1_sub[28..126] {"count":9,"merged_sample":{"26a_F040644":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":16}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:23:6103:3418#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:107:2103:10677#0/1_sub[28..127] {"count":20,"merged_sample":{"13a_F730603":20},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":22}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:1:15993:20360#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacctgcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatgccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:103:1205:6990#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||||
|
ttagccctaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:111:2380:10482#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:76:10530:11312#0/1_sub[28..126] {"count":43,"merged_sample":{"26a_F040644":43},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":69}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:40:15984:4911#0/1_sub[28..126] {"count":16,"merged_sample":{"26a_F040644":16},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":30}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:109:19171:17424#0/1_sub[28..126] {"count":2,"merged_sample":{"13a_F730603":1,"26a_F040644":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126]":"(a)->(t)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s","26a_F040644":"i"},"obiclean_weight":{"13a_F730603":1,"26a_F040644":1}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggacttctagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:77:17898:19592#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaataattcgccagaggactactagcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:32:4908:16517#0/1_sub[78..81] {"count":7,"merged_sample":{"29a_F260619":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
|
||||||
|
ccgc
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:100:8022:19461#0/1_sub[28..127] {"count":5,"merged_sample":{"29a_F260619":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":11}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaataattcgccagagaactactagcaac
|
||||||
|
agattaaacctcaaaggacttggcagtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:59:2390:15297#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||||
|
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
|
||||||
|
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:98:10839:20244#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||||
|
ttagccctaaacataaacattcaataaacaaggatgttcgccagagtactactagcaatg
|
||||||
|
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:34:13086:6440#0/1_sub[28..127] {"count":14,"merged_sample":{"13a_F730603":14},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":18}}
|
||||||
|
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
|
||||||
|
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:73:10944:14101#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":3}}
|
||||||
|
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:61:17561:21218#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:93:7569:17305#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaatcagtctataacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:55:11954:15731#0/1_sub[28..126] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gattaaacctcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||||
|
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:54:15067:12524#0/1_sub[28..126] {"count":26,"merged_sample":{"26a_F040644":26},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":49}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:6:10451:2548#0/1_sub[28..126] {"count":12,"merged_sample":{"26a_F040644":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":15}}
|
||||||
|
ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaatg
|
||||||
|
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:23:10872:20213#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||||
|
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactagcaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgccttacgtccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:98:6034:5203#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:70:2429:19509#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgccttacgtccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:65:1843:2567#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||||
|
ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:92:1339:19811#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||||
|
ttagccctaaacacaagtaattacacaaacaaaattgttcacaagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:15:13855:1746#0/1_sub[28..127] {"count":3,"merged_sample":{"15a_F730814":2,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:7:14405:19348#0/1_sub[28..127]":"(t)->(g)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":3,"29a_F260619":1}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtgcgaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:7:7092:11003#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacgtccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
@@ -0,0 +1,24 @@
|
|||||||
|
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||||
|
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
@@ -0,0 +1,24 @@
|
|||||||
|
>seq0001 {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":1,"taxid":"taxon:9992 [Marmota]@genus"}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>seq0002 {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","seq_number":2,"taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>seq0003 {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":3,"taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>seq0004 {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","seq_number":4,"taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>seq0005 {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","seq_number":5,"taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||||
|
>seq0006 {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":6,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>seq0007 {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":7,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||||
|
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>seq0008 {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":8,"taxid":"taxon:9611 [Canis]@genus"}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
@@ -0,0 +1,9 @@
|
|||||||
|
id,count,obitag_bestid,obitag_bestmatch,obitag_match_count,obitag_rank,obitag_similarity_method,seq_number,taxid,sequence
|
||||||
|
seq0001,10172,0.9797979797979798,AY227529,1,genus,lcs,1,taxon:9992 [Marmota]@genus,ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
seq0002,260,0.9405940594059405,AF154263,9,infraorder,lcs,2,taxon:35500 [Pecora]@infraorder,ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
seq0003,7146,1,AB245427,1,species,lcs,3,taxon:9860 [Cervus elaphus]@species,ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
seq0004,87,0.9494949494949495,AY227530,2,tribe,lcs,4,taxon:337730 [Marmotini]@tribe,ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
seq0005,95,0.9595959595959596,AC187326,1,subspecies,lcs,5,taxon:9615 [Canis lupus familiaris]@subspecies,ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaacagattaaacctcaaaggacttggcagtgctttatacccct
|
||||||
|
seq0006,12004,1,AJ885202,1,species,lcs,6,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
seq0007,319,1,AJ972683,1,species,lcs,7,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
seq0008,366,1,AB048590,1,genus,lcs,8,taxon:9611 [Canis]@genus,ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
@@ -0,0 +1,6 @@
|
|||||||
|
id,seq0001,seq0002,seq0003,seq0004,seq0005,seq0006,seq0007,seq0008
|
||||||
|
29a_F260619,0,337,0,0,105,5789,376,1
|
||||||
|
15a_F730814,0,0,0,0,0,8822,0,5
|
||||||
|
13a_F730603,0,0,8039,0,0,0,0,17
|
||||||
|
26a_F040644,12205,0,0,202,12,0,0,468
|
||||||
|
|
||||||
|
@@ -0,0 +1,24 @@
|
|||||||
|
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||||
|
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||||
|
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
|
||||||
|
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||||
|
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
Binary file not shown.
|
After Width: | Height: | Size: 17 KiB |
Binary file not shown.
@@ -0,0 +1,8 @@
|
|||||||
|
@param,matching,strict
|
||||||
|
@param,primer_mismatches,2
|
||||||
|
@param,indels,false
|
||||||
|
experiment,sample,sample_tag,forward_primer,reverse_primer
|
||||||
|
wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||||
|
wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||||
|
wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||||
|
wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||||
|
1530
jupyterhub_volumes/web/obidoc/docs/cookbook/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/cookbook/index.html
Normal file
File diff suppressed because it is too large
Load Diff
12
jupyterhub_volumes/web/obidoc/docs/cookbook/index.xml
Normal file
12
jupyterhub_volumes/web/obidoc/docs/cookbook/index.xml
Normal file
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Cookbook on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/cookbook/</link>
|
||||||
|
<description>Recent content in Cookbook on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
@@ -0,0 +1,102 @@
|
|||||||
|
SHELL := /bin/bash
|
||||||
|
FTPNCBI=ftp.ncbi.nlm.nih.gov
|
||||||
|
GBURL=https://$(FTPNCBI)/genbank
|
||||||
|
GBRELEASE_URL=$(GBURL)/GB_Release_Number
|
||||||
|
|
||||||
|
TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
|
||||||
|
|
||||||
|
GBRELEASE:=$(shell curl $(GBRELEASE_URL))
|
||||||
|
|
||||||
|
GBDIV_ALL:=$(shell curl -L ${GBURL} \
|
||||||
|
| grep -E 'gb.+\.seq\.gz' \
|
||||||
|
| sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
|
||||||
|
| sort \
|
||||||
|
| uniq)
|
||||||
|
|
||||||
|
GBDIV=bct inv mam phg pln pri rod vrl vrt
|
||||||
|
DIRECTORIES=fasta fasta_fgs
|
||||||
|
|
||||||
|
GBFILE_ALL:=$(shell curl -L ${GBURL} \
|
||||||
|
| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
|
||||||
|
| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
|
||||||
|
|
||||||
|
|
||||||
|
SUFFIXES += .d
|
||||||
|
NODEPS:=clean taxonomy
|
||||||
|
DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
|
||||||
|
|
||||||
|
ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
|
||||||
|
#Chances are, these files don't exist. GMake will create them and
|
||||||
|
#clean up automatically afterwards
|
||||||
|
-include $(DEPFILES)
|
||||||
|
endif
|
||||||
|
|
||||||
|
|
||||||
|
all: depends directories FORCE
|
||||||
|
@make downloads
|
||||||
|
|
||||||
|
downloads: taxonomy fasta_files
|
||||||
|
@echo Genbank Release number $(GBRELEASE)
|
||||||
|
@echo all divisions : $(GBDIV_ALL)
|
||||||
|
|
||||||
|
FORCE:
|
||||||
|
|
||||||
|
.PHONY: all directories depends taxonomy fasta_files FORCE
|
||||||
|
|
||||||
|
depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
|
||||||
|
|
||||||
|
division: $(GBDIV)
|
||||||
|
|
||||||
|
taxonomy: directories Release_$(GBRELEASE)/taxonomy
|
||||||
|
|
||||||
|
directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp
|
||||||
|
|
||||||
|
Release_$(GBRELEASE):
|
||||||
|
@mkdir -p $@
|
||||||
|
@echo Create $@ directory
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
|
||||||
|
@mkdir -p $@
|
||||||
|
@echo Create $@ directory
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
|
||||||
|
@mkdir -p $@
|
||||||
|
@echo Create $@ directory
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
|
||||||
|
@mkdir -p $@
|
||||||
|
@echo Create $@ directory
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
|
||||||
|
@echo Create depends directory
|
||||||
|
@mkdir -p Release_$(GBRELEASE)/depends
|
||||||
|
@for f in ${GBFILE_ALL} ; do \
|
||||||
|
echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
|
||||||
|
echo -e "\t@echo Downloading file : $$f..." ; \
|
||||||
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
|
||||||
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
|
||||||
|
echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@" ; \
|
||||||
|
echo ; \
|
||||||
|
div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
|
||||||
|
fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||||
|
fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||||
|
fasta_files="$$fasta_files $$fasta" ; \
|
||||||
|
fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
|
||||||
|
echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
|
||||||
|
echo -e "\t@echo converting file : \$$< in fasta" ; \
|
||||||
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
|
||||||
|
echo -e "\t@obiconvert -Z --fasta-output --skip-empty \\" ; \
|
||||||
|
echo -e "\t Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
|
||||||
|
echo -e "\t && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@ \\" ; \
|
||||||
|
echo -e "\t && rm -f Release_$(GBRELEASE)/tmp/$$f \\" ; \
|
||||||
|
echo -e "\t || rm -f \$$@" ; \
|
||||||
|
echo -e "\t@echo conversion of $$@ done." ; \
|
||||||
|
echo ; \
|
||||||
|
done > $@ ; \
|
||||||
|
echo >> $@ ; \
|
||||||
|
echo "fasta_files: $$fasta_files" >> $@ ;
|
||||||
|
|
||||||
|
Release_$(GBRELEASE)/taxonomy:
|
||||||
|
mkdir -p $@
|
||||||
|
curl -iL $(TAXOURL) \
|
||||||
|
| tar -C $@ -zxf -
|
||||||
1919
jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.html
Normal file
1919
jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Prepare a local copy of Genbank on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/cookbook/local_genbank/</link>
|
||||||
|
<description>Recent content in Prepare a local copy of Genbank on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/local_genbank/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1552
jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.html
Normal file
1552
jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.html
Normal file
File diff suppressed because it is too large
Load Diff
12
jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.xml
Normal file
12
jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.xml
Normal file
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Oxford Nanopore data analysis on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/cookbook/minion/</link>
|
||||||
|
<description>Recent content in Oxford Nanopore data analysis on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/minion/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1702
jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.html
Normal file
1702
jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Build a reference database on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/cookbook/reference_db/</link>
|
||||||
|
<description>Recent content in Build a reference database on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/reference_db/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1530
jupyterhub_volumes/web/obidoc/docs/file_format/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/file_format/index.html
Normal file
File diff suppressed because it is too large
Load Diff
11
jupyterhub_volumes/web/obidoc/docs/file_format/index.xml
Normal file
11
jupyterhub_volumes/web/obidoc/docs/file_format/index.xml
Normal file
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>File formats on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/file_format/</link>
|
||||||
|
<description>Recent content in File formats on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/file_format/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Annotation of sequences on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/file_format/sequence_files/annotations/</link>
|
||||||
|
<description>Recent content in Annotation of sequences on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/file_format/sequence_files/annotations/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>CSV format on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/</link>
|
||||||
|
<description>Recent content in CSV format on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
@@ -0,0 +1,6 @@
|
|||||||
|
>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
|
||||||
|
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||||
|
>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
|
||||||
|
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
|
||||||
|
agcttaaaactcaaaggacctggcagttctttatatccct
|
||||||
@@ -0,0 +1,8 @@
|
|||||||
|
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(T:26)->(G:13)":62,"(T:34)->(G:18)":48},"score":484,"score_norm":0.968,"seq_a_single":46,"seq_ab_match":60,"seq_b_single":46}
|
||||||
|
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
|
||||||
|
+
|
||||||
|
CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
|
||||||
|
@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(A:02)->(G:30)":104,"(A:34)->(G:14)":64,"(C:02)->(A:30)":86,"(C:02)->(T:20)":108,"(C:27)->(G:32)":83,"(C:34)->(G:18)":57,"(T:02)->(G:26)":87,"(T:22)->(G:14)":66,"(T:29)->(G:11)":62,"(T:32)->(G:30)":48},"score":283,"score_norm":0.839,"seq_a_single":46,"seq_ab_match":52,"seq_b_single":46}
|
||||||
|
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
|
||||||
|
+
|
||||||
|
CCCCCCCCCCCCCCCCCCCCCCCBBCCC?BCCCCCBC?CCCC@@;AVA`cWeb_TYC\UIN?IDP8QJMKRPVGLQAFPPc`AbAFB5A4>AAA56A><>8>>F@A><8??@BB+<?;?C@9CCCCCC<CC=CCCCCCCCCBC?CBCCCCC@CC
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Sequence file formats on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/file_format/sequence_files/</link>
|
||||||
|
<description>Recent content in Sequence file formats on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/file_format/sequence_files/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
@@ -0,0 +1,30 @@
|
|||||||
|
taxid,parent,taxonomic_rank,scientific_name
|
||||||
|
taxon:1 [root]@no rank,taxon:1 [root]@no rank,no rank,root
|
||||||
|
taxon:131567 [cellular organisms]@no rank,taxon:1 [root]@no rank,no rank,cellular organisms
|
||||||
|
taxon:2759 [Eukaryota]@superkingdom,taxon:131567 [cellular organisms]@no rank,superkingdom,Eukaryota
|
||||||
|
taxon:33090 [Viridiplantae]@kingdom,taxon:2759 [Eukaryota]@superkingdom,kingdom,Viridiplantae
|
||||||
|
taxon:35493 [Streptophyta]@phylum,taxon:33090 [Viridiplantae]@kingdom,phylum,Streptophyta
|
||||||
|
taxon:131221 [Streptophytina]@subphylum,taxon:35493 [Streptophyta]@phylum,subphylum,Streptophytina
|
||||||
|
taxon:3193 [Embryophyta]@clade,taxon:131221 [Streptophytina]@subphylum,clade,Embryophyta
|
||||||
|
taxon:58023 [Tracheophyta]@clade,taxon:3193 [Embryophyta]@clade,clade,Tracheophyta
|
||||||
|
taxon:78536 [Euphyllophyta]@clade,taxon:58023 [Tracheophyta]@clade,clade,Euphyllophyta
|
||||||
|
taxon:58024 [Spermatophyta]@clade,taxon:78536 [Euphyllophyta]@clade,clade,Spermatophyta
|
||||||
|
taxon:3398 [Magnoliopsida]@class,taxon:58024 [Spermatophyta]@clade,class,Magnoliopsida
|
||||||
|
taxon:1437183 [Mesangiospermae]@clade,taxon:3398 [Magnoliopsida]@class,clade,Mesangiospermae
|
||||||
|
taxon:71240 [eudicotyledons]@clade,taxon:1437183 [Mesangiospermae]@clade,clade,eudicotyledons
|
||||||
|
taxon:91827 [Gunneridae]@clade,taxon:71240 [eudicotyledons]@clade,clade,Gunneridae
|
||||||
|
taxon:1437201 [Pentapetalae]@clade,taxon:91827 [Gunneridae]@clade,clade,Pentapetalae
|
||||||
|
taxon:71275 [rosids]@clade,taxon:1437201 [Pentapetalae]@clade,clade,rosids
|
||||||
|
taxon:91835 [fabids]@clade,taxon:71275 [rosids]@clade,clade,fabids
|
||||||
|
taxon:3502 [Fagales]@order,taxon:91835 [fabids]@clade,order,Fagales
|
||||||
|
taxon:3514 [Betulaceae]@family,taxon:3502 [Fagales]@order,family,Betulaceae
|
||||||
|
taxon:3504 [Betula]@genus,taxon:3514 [Betulaceae]@family,genus,Betula
|
||||||
|
taxon:1685988 [Betula murrayana]@species,taxon:3504 [Betula]@genus,species,Betula murrayana
|
||||||
|
taxon:361422 [Betula ovalifolia]@species,taxon:3504 [Betula]@genus,species,Betula ovalifolia
|
||||||
|
taxon:1685972 [Betula x caerulea]@species,taxon:3504 [Betula]@genus,species,Betula x caerulea
|
||||||
|
taxon:216986 [Betula schmidtii]@species,taxon:3504 [Betula]@genus,species,Betula schmidtii
|
||||||
|
taxon:312791 [Betula michauxii]@species,taxon:3504 [Betula]@genus,species,Betula michauxii
|
||||||
|
taxon:3015411 [Betula pamirica]@species,taxon:3504 [Betula]@genus,species,Betula pamirica
|
||||||
|
taxon:312792 [Betula raddeana]@species,taxon:3504 [Betula]@genus,species,Betula raddeana
|
||||||
|
taxon:216991 [Betula humilis]@species,taxon:3504 [Betula]@genus,species,Betula humilis
|
||||||
|
taxon:2218489 [Betula ovalifolia x Betula ermanii]@species,taxon:3504 [Betula]@genus,species,Betula ovalifolia x Betula ermanii
|
||||||
|
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>CSV formatted taxdump on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/file_format/taxonomy_file/csv_taxdump/</link>
|
||||||
|
<description>Recent content in CSV formatted taxdump on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/file_format/taxonomy_file/csv_taxdump/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Taxonomy file formats on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/file_format/taxonomy_file/</link>
|
||||||
|
<description>Recent content in Taxonomy file formats on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/file_format/taxonomy_file/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>NCBI taxdump on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/</link>
|
||||||
|
<description>Recent content in NCBI taxdump on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1530
jupyterhub_volumes/web/obidoc/docs/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/index.html
Normal file
File diff suppressed because it is too large
Load Diff
19
jupyterhub_volumes/web/obidoc/docs/index.xml
Normal file
19
jupyterhub_volumes/web/obidoc/docs/index.xml
Normal file
@@ -0,0 +1,19 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Docs on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/</link>
|
||||||
|
<description>Recent content in Docs on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate>Mon, 01 Jan 0001 00:00:00 +0000</lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
<item>
|
||||||
|
<title>About</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/about/</link>
|
||||||
|
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
|
||||||
|
<guid>http://metabar:8888/obidoc/docs/about/</guid>
|
||||||
|
<description><h2 id="what-are-obitools4">
 What are OBITools4?
 <a class="anchor" href="#what-are-obitools4">#</a>
</h2>
<p>The development of <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 began at 
 <a href="https://leca.osug.fr"><abbr title="LECA: Laboratoire d&#39;écologie Alpine - Laboratory for Alpine Ecology">LECA</abbr>
 
 </a> (
 <a href="https://www.univ-grenoble-alpes.fr/">University of Grenoble</a>) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as <code>grep</code>, <code>uniq</code> or <code>wc</code>, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.</p></description>
|
||||||
|
</item>
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1638
jupyterhub_volumes/web/obidoc/docs/installation/index.html
Normal file
1638
jupyterhub_volumes/web/obidoc/docs/installation/index.html
Normal file
File diff suppressed because it is too large
Load Diff
12
jupyterhub_volumes/web/obidoc/docs/installation/index.xml
Normal file
12
jupyterhub_volumes/web/obidoc/docs/installation/index.xml
Normal file
@@ -0,0 +1,12 @@
|
|||||||
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>Installation on OBITools4 documentation</title>
|
||||||
|
<link>http://metabar:8888/obidoc/docs/installation/</link>
|
||||||
|
<description>Recent content in Installation on OBITools4 documentation</description>
|
||||||
|
<generator>Hugo</generator>
|
||||||
|
<language>en-us</language>
|
||||||
|
<lastBuildDate></lastBuildDate>
|
||||||
|
<atom:link href="http://metabar:8888/obidoc/docs/installation/index.xml" rel="self" type="application/rss+xml" />
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
1638
jupyterhub_volumes/web/obidoc/docs/patterns/dnagrep/index.html
Normal file
1638
jupyterhub_volumes/web/obidoc/docs/patterns/dnagrep/index.html
Normal file
File diff suppressed because it is too large
Load Diff
1530
jupyterhub_volumes/web/obidoc/docs/patterns/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/patterns/index.html
Normal file
File diff suppressed because it is too large
Load Diff
25
jupyterhub_volumes/web/obidoc/docs/patterns/index.xml
Normal file
25
jupyterhub_volumes/web/obidoc/docs/patterns/index.xml
Normal file
File diff suppressed because one or more lines are too long
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user