push-uzomzootkrpy #5
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/jupyterhub_volumes/shared
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/jupyterhub_volumes/jupyterhub
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/jupyterhub_volumes/caddy
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/jupyterhub_volumes/course/data/Genbank
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/**/.DS_Store
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/web_src/**/*.RData
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/web_src/**/*.pdf
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/web_src/**/*_files
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/web_src/**/*_cache
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/.luarc.json
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/sandbox
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*.log
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ncbitaxo_*
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{"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$"}
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---
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title: "Designing Fish primers"
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format: revealjs
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editor: visual
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---
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```{r setup, include=FALSE}
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library(knitr)
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```
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# Preparing the data
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------------------------------------------------------------------------
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## What do we need ?
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To design a new animal DNA metabarcode we download from the NCBI the following data
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- The complete set of whole mitochondrial genomes
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- The NCBI taxonomy
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------------------------------------------------------------------------
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## We need also:
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- a Unix computer: a Mac or a Linux box
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- A unix terminal window for typing commands
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- Installed on the computer
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- The OBITools --- <http://github.com/metabarcoding/obitools4>
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- ecoPrimers --- <http://metabarcoding.org/ecoprimers>
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- R --- <http://wwww.r-project.org>
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------------------------------------------------------------------------
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## Downloading the mitochondrial genomes
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We can use an internet browser and download the files from NCBI FTP website
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{fig-align="center"}
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------------------------------------------------------------------------
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## Downloading the mitochondrial genomes
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We can use an internet browser and download the files from NCBI FTP website
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or run the following command lines
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```{bash}
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#| eval: false
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#| echo: true
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curl 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/mitochondrion/mitochondrion.1.genomic.gbff.gz' \
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> mito.all.gb.gz
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```
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------------------------------------------------------------------------
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```{bash}
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#| eval: false
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#| echo: true
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zless mito.all.gb.gz
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```
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```
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LOCUS NW_009243181 45189 bp DNA linear CON 06-OCT-2014
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DEFINITION Fonticula alba strain ATCC 38817 mitochondrial scaffold
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supercont2.211, whole genome shotgun sequence.
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ACCESSION NW_009243181 NZ_AROH01000000
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VERSION NW_009243181.1
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DBLINK BioProject: PRJNA262900
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Assembly: GCF_000388065.1
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KEYWORDS WGS; RefSeq.
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SOURCE mitochondrion Fonticula alba
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ORGANISM Fonticula alba
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Eukaryota; Rotosphaerida; Fonticulaceae; Fonticula.
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REFERENCE 1 (bases 1 to 45189)
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```
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------------------------------------------------------------------------
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## Downloading the complete taxonomy
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```{bash}
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#| eval: false
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#| echo: true
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obitaxonomy --download-ncbi
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```
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```
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INFO[0000] Number of workers set 16
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INFO[0000] Downloading NCBI Taxdump to ncbitaxo_20250211.tgz
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downloading 100% ████████████████████████████████████████| (66/66 MB, 5.1 MB/s)
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```
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The NCBI taxonomy contains all the relationship between taxa. Each taxon is identified by a unique numerical id: `taxid`
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------------------------------------------------------------------------
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## The archive contains several files
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file: `nodes.dmp`
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```
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1 | 1 | no rank | | 8 | 0 | ...
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2 | 131567 | superkingdom | | 0 | 0 |
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6 | 335928 | genus | | 0 | 1 |
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7 | 6 | species | AC | 0 | 1 |
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9 | 32199 | species | BA | 0 |
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10 | 135621 | genus | | 0 |
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11 | 1707 | species | CG | 0 | 1 |
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13 | 203488 | genus | | 0 | 1 |
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14 | 13 | species | DT | 0 | 1 |
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```
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------------------------------------------------------------------------
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## file: `names.dmp`
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```
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1 | root | | scientific name |
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2 | Bacteria | Bacteria <prokaryote> | scientific name |
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2 | Monera | Monera <Bacteria> | in-part |
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2 | Procaryotae | Procaryotae <Bacteria> | in-part |
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2 | Prokaryota | Prokaryota <Bacteria> | in-part |
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2 | Prokaryotae | Prokaryotae <Bacteria> | in-part |
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2 | bacteria | bacteria <blast2> | blast name |
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2 | eubacteria | | genbank common name |
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2 | prokaryote | prokaryote <Bacteria> | in-part |
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...
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10 | Cellvibrio | | scientific name |
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11 | [Cellvibrio] gilvus | | scientific name |
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13 | Dictyoglomus | | scientific name |
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14 | Dictyoglomus thermophilum | | scientific name |
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```
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------------------------------------------------------------------------
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## Preparing the set of complete genomes
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```{bash}
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#| eval: false
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#| echo: true
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obiconvert --skip-empty \
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--update-taxid \
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-t ncbitaxo_20250211.tgz \
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mito.all.gb.gz \
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> mito.all.fasta
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head -5 mito.all.fasta
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```
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five first lines of the new `mito.all.fasta` file
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```
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>NC_072933 {"definition":"Echinosophora koreensis mitochondrion, complete genome.","scientific_name":"mitochondrion Echinosophora koreensis","taxid":228658}
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ctttcgggtcggaaatagaagatctggattagatcccttctcgatagctttagtcagagc
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tcatccctcgaaaaagggagtagtgagatgagaaaagggtgactagaatacggaaattca
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actagtgaagtcagatccgggaattccactattgaagttatccgtcttaggcttcaagca
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agctatctttcaaggaagtcagtctaagccctaagccaagatctgctttttgccagtcaa
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```
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------------------------------------------------------------------------
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## We want:
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- annotate sequences by their species `taxid`
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- keep a single genome per species
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- extract only vertebrate genome
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------------------------------------------------------------------------
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## Looking for the **Vertebrata**'s taxid
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```{bash}
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#| eval: false
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#| echo: true
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obitaxonomy -t ncbitaxo_20250211.tgz \
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--fixed \
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'vertebrata'
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```
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``` csv
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taxid,parent,taxonomic_rank,scientific_name
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taxon:1261581 [Vertebrata]@genus,taxon:2008651 [Polysiphonioideae]@subfamily,genus,Vertebrata
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taxon:7742 [Vertebrata]@clade,taxon:89593 [Craniata]@subphylum,clade,Vertebrata
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```
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------------------------------------------------------------------------
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## Looking for the **Vertebrata**'s taxid
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```{bash}
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#| eval: false
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#| echo: true
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obitaxonomy -t ncbitaxo_20250211.tgz \
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--fixed \
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'vertebrata' \
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| csvlook
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```
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``` csv
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| taxid | parent | taxonomic_rank | scientific_name |
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| -------------------------------- | ------------------------------------------- | -------------- | --------------- |
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| taxon:1261581 [Vertebrata]@genus | taxon:2008651 [Polysiphonioideae]@subfamily | genus | Vertebrata |
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| taxon:7742 [Vertebrata]@clade | taxon:89593 [Craniata]@subphylum | clade | Vertebrata |
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```
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## A genus called **Vertebrata**
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```{bash}
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#| eval: false
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#| echo: true
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obitaxonomy -t ncbitaxo_20250211.tgz \
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-p 2008651 \
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| csvlook
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```
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``` csv
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| taxid | parent | taxonomic_rank | scientific_name |
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||||
| ------------------------------------------- | ------------------------------------------- | -------------- | ------------------ |
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| taxon:2008651 [Polysiphonioideae]@subfamily | taxon:2803 [Rhodomelaceae]@family | subfamily | Polysiphonioideae |
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| taxon:2803 [Rhodomelaceae]@family | taxon:2802 [Ceramiales]@order | family | Rhodomelaceae |
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| taxon:2802 [Ceramiales]@order | taxon:2045261 [Rhodymeniophycidae]@subclass | order | Ceramiales |
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| taxon:2045261 [Rhodymeniophycidae]@subclass | taxon:2806 [Florideophyceae]@class | subclass | Rhodymeniophycidae |
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| taxon:2806 [Florideophyceae]@class | taxon:2763 [Rhodophyta]@phylum | class | Florideophyceae |
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| taxon:2763 [Rhodophyta]@phylum | taxon:2759 [Eukaryota]@superkingdom | phylum | Rhodophyta |
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| taxon:2759 [Eukaryota]@superkingdom | taxon:131567 [cellular organisms]@no rank | superkingdom | Eukaryota |
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| taxon:131567 [cellular organisms]@no rank | taxon:1 [root]@no rank | no rank | cellular organisms |
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| taxon:1 [root]@no rank | taxon:1 [root]@no rank | no rank | root |
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```
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------------------------------------------------------------------------
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## Reannotation and selection of the genomes
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```{bash}
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#| eval: false
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#| echo: true
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obiannotate -t ncbitaxo_20250211.tgz \
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--with-taxon-at-rank=species \
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mito.all.fasta | \
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obiannotate -S 'ori_taxid=annotations.taxid' | \
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obiannotate -S 'taxid=annotations.species_taxid' | \
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obiuniq -c taxid > mito.one.fasta
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```
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------------------------------------------------------------------------
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## Species representation
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||||
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```{bash}
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#| eval: false
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#| echo: true
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obicsv -k taxid mito.one.fasta \
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| tail -n +2 \
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| sort \
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| uniq -c \
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| sort -nk1 \
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| cut -w -f 2 \
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| uplot count
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```
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```
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┌ ┐
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1 ┤■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 17769.0
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2 ┤ 90.0
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3 ┤ 17.0
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4 ┤ 5.0
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5 ┤ 4.0
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6 ┤ 2.0
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7 ┤ 1.0
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└ ┘
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```
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------------------------------------------------------------------------
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## Selection of the vertebrata genomes
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```{bash}
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#| eval: false
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#| echo: true
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obigrep -t ncbitaxo_20250211.tgz \
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-r 7742 \
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mito.one.fasta > mito.vert.fasta
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```
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```{bash}
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#| eval: false
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#| echo: true
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obicount mito.vert.fasta \
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| csvlook
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```
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```
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| entities | n |
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| -------- | ----------- |
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| variants | 7,822 |
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| reads | 7,823 |
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| symbols | 131,378,756 |
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```
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------------------------------------------------------------------------
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## Prepare data for ecoPrimers 1/3
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```{bash}
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#| eval: false
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#| echo: true
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mkdir ncbitaxo_20250211
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cd ncbitaxo_20250211
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tar zxvf ../ncbitaxo_20250211.tgz
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cd ..
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```
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------------------------------------------------------------------------
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||||
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## Prepare data for ecoPrimers 2/3
|
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|
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```{bash}
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#| eval: false
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#| echo: true
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obiconvert -O mito.vert.fasta > mito.vert.old.fasta
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```
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```{bash}
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#| eval: false
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#| echo: true
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head -5 mito.vert.old.fasta
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```
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``` csv
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>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.
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gctagcgtagcttaaccaaagcataacactgaagatgttaagatgggccctagaaagccc
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cgcaagcacaaaagcttggtcctggctttactatcagcttaggctaaacttacacatgca
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agtatccgcatccccgtgagaatgcccttaagctcccaccgctaacaggagtcaaggagc
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cggtatcaggcacaaccctgagttagcccacgacaccttgctcagccacacccccaaggg
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```
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------------------------------------------------------------------------
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||||
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||||
## Prepare data for ecoPrimers 3/3
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||||
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```{bash}
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#| eval: false
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||||
#| echo: true
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ecoPCRFormat -t ncbitaxo_20250211 \
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-f \
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-n vertebrata \
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mito.vert.old.fasta
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||||
```
|
||||
|
||||
```{bash}
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||||
#| eval: false
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||||
#| echo: true
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ls -l vertebrata*
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||||
```
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||||
|
||||
```
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||||
-rw-r--r--@ 1 coissac staff 260899785 Feb 11 11:53 vertabrata.ndx
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||||
-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
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||||
-rw-r--r--@ 1 coissac staff 40446318 Feb 11 11:54 vertabrata_001.sdx
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||||
```
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||||
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------------------------------------------------------------------------
|
||||
|
||||
## Looking for the *Teleostei* `taxid`
|
||||
|
||||
```{bash}
|
||||
#| eval: false
|
||||
#| echo: true
|
||||
obitaxonomy -t ncbitaxo_20250211.tgz \
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||||
--fixed \
|
||||
'Teleostei' \
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||||
| csvlook
|
||||
```
|
||||
|
||||
``` csv
|
||||
| taxid | parent | taxonomic_rank | scientific_name |
|
||||
| ---------------------------------- | ---------------------------------- | -------------- | --------------- |
|
||||
| taxon:32443 [Teleostei]@infraclass | taxon:41665 [Neopterygii]@subclass | infraclass | Teleostei |
|
||||
```
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||||
|
||||
------------------------------------------------------------------------
|
||||
|
||||
## Selecting the best primer pairs
|
||||
|
||||
```{bash}
|
||||
#| eval: false
|
||||
#| echo: true
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||||
ecoPrimers -d vertebrata \
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||||
-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))
|
||||
```
|
||||
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,153 @@
|
||||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 3,
|
||||
"id": "7855cd6e-63d4-422c-9c42-1cb02be29702",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"scores <- read.csv(\"wolf_paired_scores.csv\", header = TRUE)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 4,
|
||||
"id": "27b28f13-8f6f-448a-9e82-acf3eeee42ca",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"image/png": "iVBORw0KGgoAAAANSUhEUgAAA0gAAANICAMAAADKOT/pAAADAFBMVEUAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACz\nMPSIAAABAHRSTlMAAQIDBAUGBwgJCgsMDQ4PEBESExQVFhcYGRobHB0eHyAhIiMkJSYnKCkq\nKywtLi8wMTIzNDU2Nzg5Ojs8PT4/QEFCQ0RFRkdISUpLTE1OT1BRUlNUVVZXWFlaW1xdXl9g\nYWJjZGVmZ2hpamtsbW5vcHFyc3R1dnd4eXp7fH1+f4CBgoOEhYaHiImKi4yNjo+QkZKTlJWW\nl5iZmpucnZ6foKGio6SlpqeoqaqrrK2ur7CxsrO0tba3uLm6u7y9vr/AwcLDxMXGx8jJysvM\nzc7P0NHS09TV1tfY2drb3N3e3+Dh4uPk5ebn6Onq6+zt7u/w8fLz9PX29/j5+vv8/f7/qVjM\n+gAAAAlwSFlzAAASdAAAEnQB3mYfeAAAIABJREFUeJzsnQd8FMUXxychhA4RaYIoXURQqlgQ\nRJpiRfGPIoIiCqKACIogCjZEUEQ6gihIR6o0QXqXXkIAExJIJb1e3Z3339mZvUByuVy8y+3d\n5X0/n2Te7c7tvtvb383slDeEIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiC\nIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiC\nIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiC\nIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiC\nIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCIAiCeB8PtEEQn+IBvTVjj7aA\nID5GW71VY4dHIFhvFxCkKATDI3q7YAcUEuJjoJAQxA14XkiV69wRWFgeFBLiY3hYSM0XxyuP\nZVLM8kcdZkMhIT6GZ4U0k0Lc0S1bjkQDLHCUD4WE+BgeFdJQ2N6KW/ethA8dZEQhIT6GR4V0\n6FKQZgbsP+ggIwoJ8TE8KqSM33Ltb9IdZEQhIT6GZ0uksFI2ezeWSIgf4eFnpK0tuNVkGXzk\nICMKCfExPNtqNxfg+oGNG/ZdBfg1wEE+FBLiY3i4H6nl8iTWjxS3vJPDbCgkxMfw/MiGkLq1\ncGQD4m/gECEEcQM4RAhB3AAOEUIQN+BbQ4Tun7xly+T7/+PZq4xYtmf+K6UKz3gzraZs3fzt\nfTdtKDto0d5f3y5705ZnDyckHeurGNlKYUs3KCfanW7NOtmAkNtGLt8972WlIpvCZlDKShaZ\nGRIhoZTlNRJiUI2thLTfHZNyZpSWxUTIBHWPmZAM1UghxKIaSpaFZkrNvytGj5l/r/m0NiFV\n96VbM/+pe5NTTb7e+Nf37RVj+OmU2L3Kd1x2Zlha5No6N2UZnC5Rw1rF+DrBYop+Q8lyzESl\nhK6E1FgennZ5YUVCuocbLMm/KllafqdchuaElFqaYjVc6URI9UPp1oyjyqmrf7Ry95znAwi5\n95tN26eyWaI32GddRMiDqrtjCFmvGm0I2c8+mvJByLIcKqUrN0Dw5lRr9vmWhIxQszxIyCXt\nM46LM5tihhAS+NWF1OtbmxLSLFEGObGxoy8reMDCvUuGViDkuUwK0r/lCelyID75xNvKrn+V\n41LFqeqZyvEtrxDyk3qihwiZZFXcPa9kSWfe/UtINXXPSUJeZoasODU4RzncGSXLqFizOXaU\n/XP70hChT6R9U6bskz75TydvHXPt54krsg7eVpQ3TZD2fDf1oDVX9HeFJv028bfEi/VsW9ZB\n5vEjqbC/iZhxbOkgQ3ZUOtChD8ZHzp+4KntPZSp2vSVSamT/2LckC8M8FYxnDiZAeLCWJUsY\nsiSyWLWjnFR2WcwAhtIrzRu+nHUh45nuMmRFZQAdaHNqsPnotG93yFODwiDx0BkDzGiYSaP2\nXpKkPrYsZ5QjZMpgLhsPltgbMhxtrtwt6SaA5d0t8pW9EdTQcgXQ5GsmyKkyXtr73ZQD0kfV\njWCMSqHw63MUMtkZX+2UfGXuF38Yt5Z/33L4+8m75G9qCS+zlwm/Yy3CWCWJXZUNIGfmAFxu\naoWcqDQKX17Tsmif8aFrYI1NkOBs1QSI2RdqpqMmKpfCpFyujwv+smqdSvt94i9xEU23sbzK\noR79DbJPHkmGkyHs+MqGrIHiREezhbElkV9iWlW78LO17+aIMNYoV0pSDkfrXgZrXJwVLts7\nuS8NEept7sWSXuaX/sO5K8f9XkZJ6pzdVIQ3vWZ6hiV9LM+IDaVO7QpRkio7zmo/CZ/BLJ4A\nRClpeeWCS+yS1jXS5F/Yp6gbKqs/sUpRQ9VSiaiyUNJE9sVFKwa71bazFpi+Mv85VrMoBReJ\nZFkMimFixmuKwe7GcJblImTEKWUECfjSIEntFKOBiVYVTj1uVTX1RPZF+iYzNkKGQfndJyGR\n0h0iy0yIZ8lCsMJsZhwAGd5V0momsCbUVIzGGUaIYuX3cEgzPcey9LZkwDtKGhwL1MoO19RM\n039iWRpGbLf2Y1l6GADYr3tZ9gvBSrtXmd9KAUCiRElDkpXLsIqoWyTKjluVFQXMX1V67PIq\nB4ElLMsOSLd2Y2c8qVyQLorRHaBKQV9WwIHD1ZSkwoY4kNmnHKucSD3KcEVDzCn1On+rpC2Y\nU6ycOs5+w9ie3Upek3bh2Z3ZlWVRCkTyNcuilG1krpJlHcuyDjbaObsvDRE6NZWnU0/+h3OP\nuF5GTVtAC+ffFPo1T2ccFhueMdRQ0+rZL4gtGedFVvXGVwDgv/qNwVhaNdoA8D2U30ksiyoo\npqQ01ZC0LPNys3Bjj/im2U3wqDiKyGsG8YMSD0+Lj7ZDOPXXrzwdD4u5kQ7PqmlVabXIInEX\nSDhc4YYRlqmp8uvN64jthZeKDH/mxjJYoaalKDyhGu0gk7fAdua3LCGL+P3IPsBFNX2X64i5\na7sM8cIF+ExNqwCMUI1TuVnSNb/HqGkQhZdV4w0Q1zs/Ha13q6lSAaimGpvF1SV/5Tq1U02V\nr2SsaqRoZ8zI+920B5igGmu0LGGQyo142c7ZvWeIUODjXW2MsCekivAQNx6mFYp+7j/mCuPy\nu06/53YQj3SPy8Kf77Rbdev3PC0Lo7mRDUO5QcV1J1bx7RHtO5I1rdmyAOTJEp+bZUbeLMJY\nreU9CD24kSI2EEOKMHK4bMiH8Bg3IrWjhF3TDhfG04ma+jK0LLLtjNk8raeWLYQVEKJebLXl\nFVlKgfjJiYb+hX3GsxDLjawCs8zQNHwGKuU9nJkUwKdHtSzajQ5ZPD0N8wtzKlQt99Us9fJm\nEUZ77QfgWy3LzXjPEKH6iak2csCOVO6AJty4B+7Iv7cwdnwjjCPOP2LVA/4bR+4HUWmau1Ls\nWipaHevAq9wwqVUPctOXZbHwtGqukOQ8WfJ9WUbtR5RqpUC+LK9qh1ujaThdE1KauK1LU9G7\nMA5ac+OqdpQjidrh9vN0DOzmRoZWaZJsZ8zkaV34ixsHoDo3bEKSjDytAF9xIxXuKcBv2z27\nSftlz4SgAvL21/Ieh6bcsF0yKn5p8vPdVu0oIkuQJo5weD/PUfI5FZN74Z8swKmuIK7dIOia\n/+zeOURoMFTMv7G0sSc3nhZ1piKxaBVPAxNfc/o95SxCHC9mCdl/ekLsOva5OBydxo0kWM8N\n25cli5ssyI6QQrmR7/s8kJslI28Wm9ZE3jBow41EWxkofupJ/ACeDoVe3LgGohM8Nkw7XBxP\nZ8J2bmRArTwfAHJ42kmrILine truncated
|
||||
"text/plain": [
|
||||
"plot without title"
|
||||
]
|
||||
},
|
||||
"metadata": {
|
||||
"image/png": {
|
||||
"height": 420,
|
||||
"width": 420
|
||||
}
|
||||
},
|
||||
"output_type": "display_data"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"plot(scores)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"id": "0114755c-beb6-4c97-bd32-43e2888788ed",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"image/png": "iVBORw0KGgoAAAANSUhEUgAAA0gAAANICAYAAAD958/bAAAACXBIWXMAABJ0AAASdAHeZh94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\nAAAAAAAAAAAAAAAAAAAAALine truncated
|
||||
"text/plain": [
|
||||
"Plot with title “Histogram of scores$ali_length”"
|
||||
]
|
||||
},
|
||||
"metadata": {
|
||||
"image/png": {
|
||||
"height": 420,
|
||||
"width": 420
|
||||
}
|
||||
},
|
||||
"output_type": "display_data"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"hist(scores$ali_length)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 6,
|
||||
"id": "36a084e3-d084-4a14-9fcc-b4cabba0ef64",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"image/png": 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truncated
|
||||
"text/plain": [
|
||||
"Plot with title “Histogram of scores$score_norm”"
|
||||
]
|
||||
},
|
||||
"metadata": {
|
||||
"image/png": {
|
||||
"height": 420,
|
||||
"width": 420
|
||||
}
|
||||
},
|
||||
"output_type": "display_data"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"hist(scores$score_norm)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 7,
|
||||
"id": "58141d2c-b523-48db-8b82-80de70886406",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"ratio <- read.csv(\"wolf_ratio.csv\",header = TRUE)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 9,
|
||||
"id": "9f4db6ec-50d8-43de-9b73-cc535ad58596",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"image/png": "iVBORw0KGgoAAAANSUhEUgAAA0gAAANICAYAAAD958/bAAAACXBIWXMAABJ0AAASdAHeZh94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\nXC9XvTRb6xa6RmCYe4clKLine truncated
|
||||
"text/plain": [
|
||||
"Plot with title “Histogram of log10(ratio$Mutant_Count/ratio$Origin_Count)”"
|
||||
]
|
||||
},
|
||||
"metadata": {
|
||||
"image/png": {
|
||||
"height": 420,
|
||||
"width": 420
|
||||
}
|
||||
},
|
||||
"output_type": "display_data"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"hist(log10(ratio$Mutant_Count/ratio$Origin_Count))"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "7d58de3d-ca00-4911-b966-06c2bfb0fc37",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
}
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truncated
|
||||
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truncated
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"type": "mesh3d",
|
||||
"frame": null
|
||||
}
|
||||
],
|
||||
"highlight": {
|
||||
"on": "plotly_click",
|
||||
"persistent": false,
|
||||
"dynamic": false,
|
||||
"selectize": false,
|
||||
"opacityDim": 0.20000000000000001,
|
||||
"selected": {
|
||||
"opacity": 1
|
||||
},
|
||||
"debounce": 0
|
||||
},
|
||||
"shinyEvents": ["plotly_hover", "plotly_click", "plotly_selected", "plotly_relayout", "plotly_brushed", "plotly_brushing", "plotly_clickannotation", "plotly_doubleclick", "plotly_deselect", "plotly_afterplot", "plotly_sunburstclick"],
|
||||
"base_url": "https://plot.ly"
|
||||
}
|
||||
+149
@@ -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�rieur � 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")
|
||||
|
||||
```
|
||||
BIN
Binary file not shown.
|
After Width: | Height: | Size: 27 KiB |
+2095
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+11
@@ -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>
|
||||
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>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>
|
||||
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>
|
||||
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|
||||
<?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>
|
||||
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|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
|
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<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
|
||||
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|
||||
<?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>
|
||||
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@@ -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'])
|
||||
|
||||
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 |
@@ -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 -
|
||||
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 |
Binary file not shown.
File diff suppressed because it is too large.
Load diff
File diff suppressed because it is too large.
Load diff
File diff suppressed because it is too large.
Load diff
+26
@@ -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
|
||||
+155744
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+5864
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+2140
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+5864
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+24
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|
||||
>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
|
||||
+329
@@ -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
|
||||
+24
@@ -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
|
||||
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|
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|
||||
@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
|
||||
|
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@@ -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 -
|
||||
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@@ -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>
|
||||
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@@ -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>
|
||||
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@@ -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>
|
||||
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@@ -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>
|
||||
+1552
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@@ -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
|
||||
Loaded 100 of 423 files, more files were not shown because too many files have changed in this diff.
Show more
Reference in new issue
Block a user