Add pedagogic content
This commit is contained in:
Eric Coissac
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.gitignore
vendored
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.gitignore
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/web_src/**/*_files
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/web_src/**/*_files
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/web_src/**/*_cache
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/web_src/**/*_cache
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/.luarc.json
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/.luarc.json
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*.log
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862
fish-primers.qmd
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862
fish-primers.qmd
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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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```{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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## Prepare data for ecoPrimers 2/3
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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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||||||
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## Prepare data for ecoPrimers 3/3
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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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```
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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
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-rw-r--r--@ 1 coissac staff 121379751 Feb 11 11:53 vertabrata.tdx
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||||||
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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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||||||
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||||||
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## Looking for the *Teleostei* `taxid`
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||||||
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|
||||||
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```{bash}
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#| eval: false
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||||||
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#| echo: true
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||||||
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obitaxonomy -t ncbitaxo_20250211.tgz \
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--fixed \
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'Teleostei' \
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||||||
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| csvlook
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||||||
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```
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||||||
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|
||||||
|
``` csv
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||||||
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| taxid | parent | taxonomic_rank | scientific_name |
|
||||||
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| ---------------------------------- | ---------------------------------- | -------------- | --------------- |
|
||||||
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| taxon:32443 [Teleostei]@infraclass | taxon:41665 [Neopterygii]@subclass | infraclass | Teleostei |
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||||||
|
```
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|
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||||||
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------------------------------------------------------------------------
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||||||
|
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||||||
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## Selecting the best primer pairs
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
ecoPrimers -d vertebrata \
|
||||||
|
-e 3 -3 2 \
|
||||||
|
-l 30 -L 150 \
|
||||||
|
-r 32443 \
|
||||||
|
-c > Teleostei.ecoprimers
|
||||||
|
```
|
||||||
|
|
||||||
|
- Total pair count : 9407
|
||||||
|
- Total good pair count : 407
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
head -35 Teleostei.ecoprimers
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
#
|
||||||
|
# ecoPrimer version 0.5
|
||||||
|
# Rank level optimisation : species
|
||||||
|
# max error count by oligonucleotide : 3
|
||||||
|
#
|
||||||
|
# Restricted to taxon:
|
||||||
|
# 32443 : Teleostei (infraclass)
|
||||||
|
#
|
||||||
|
# strict primer quorum : 0.70
|
||||||
|
# example quorum : 0.90
|
||||||
|
# counterexample quorum : 0.10
|
||||||
|
#
|
||||||
|
# database : vertebrata
|
||||||
|
# Database is constituted of 3909 examples corresponding to 3876 species
|
||||||
|
# and 0 counterexamples corresponding to 0 species
|
||||||
|
#
|
||||||
|
# amplifiat length between [30,150] bp
|
||||||
|
# DB sequences are considered as circular
|
||||||
|
# Pairs having specificity less than 0.60 will be ignored
|
||||||
|
#
|
||||||
|
0 AGAGTGACGGGCGGTGTG CGTCAGGTCGAGGTGTAG 62.8 42.4 57.5 34.1 12 11 GG 3864 0 0.988 3832 0 0.989 2731 0.713 134 146 138.22
|
||||||
|
1 CGTCAGGTCGAGGTGTAG GAGTGACGGGCGGTGTGT 57.5 34.1 63.1 42.9 11 12 GG 3863 0 0.988 3831 0 0.988 2730 0.713 133 145 137.22
|
||||||
|
2 CGTCAGGTCGAGGTGTAG GGGAGAGTGACGGGCGGT 57.5 34.1 64.5 37.0 11 13 GG 3811 0 0.975 3779 0 0.975 2689 0.712 137 149 141.22
|
||||||
|
3 CGTCAGGTCGAGGTGTAG GGGGAGAGTGACGGGCGG 57.5 34.1 65.5 38.4 11 14 GG 3804 0 0.973 3772 0 0.973 2682 0.711 138 149 142.22
|
||||||
|
4 ACACCGCCCGTCACTCTC ACCTTCCGGTACACTTAC 62.5 36.8 54.0 16.6 12 9 GG 3850 0 0.985 3818 0 0.985 2658 0.696 46 132 66.51
|
||||||
|
5 AACGTCAGGTCGAGGTGT AGAGTGACGGGCGGTGTG 58.8 28.4 62.8 41.7 10 12 GG 3779 0 0.967 3746 0 0.966 2653 0.708 137 148 140.23
|
||||||
|
6 ACACCGCCCGTCACTCTC CACCTTCCGGTACACTTA 62.5 36.8 54.0 16.6 12 9 GG 3846 0 0.984 3814 0 0.984 2654 0.696 47 133 67.51
|
||||||
|
7 AACGTCAGGTCGAGGTGT GAGTGACGGGCGGTGTGT 58.8 28.4 63.1 42.1 10 12 GG 3778 0 0.966 3745 0 0.966 2652 0.708 136 147 139.23
|
||||||
|
8 ACCTTCCGGTACACTTAC CACACCGCCCGTCACTCT 54.0 16.6 62.8 37.3 9 12 GG 3845 0 0.984 3813 0 0.984 2653 0.696 47 133 67.51
|
||||||
|
9 ACACCGCCCGTCACTCTC TCCGGTACACTTACCATG 62.5 36.8 54.1 18.1 12 9 GG 3851 0 0.985 3819 0 0.985 2651 0.694 42 128 62.51
|
||||||
|
10 ACACCGCCCGTCACTCTC CCGGTACACTTACCATGT 62.5 36.8 54.4 18.6 12 9 GG 3851 0 0.985 3819 0 0.985 2651 0.694 41 127 61.51
|
||||||
|
11 ACACCGCCCGTCACTCTC CCAAGTGCACCTTCCGGT 62.5 36.8 60.7 28.9 12 11 GG 3837 0 0.982 3805 0 0.982 2650 0.696 54 140 74.51
|
||||||
|
12 ACACCGCCCGTCACTCTC GCACCTTCCGGTACACTT 62.5 36.8 57.7 22.5 12 10 GG 3842 0 0.983 3810 0 0.983 2650 0.696 48 134 68.51
|
||||||
|
13 ACACCGCCCGTCACTCTC CGGTACACTTACCATGTT 62.5 36.8 52.4 15.7 12 8 GG 3850 0 0.985 3818 0 0.985 2650 0.694 40 126 60.51
|
||||||
|
14 ACACCGCCCGTCACTCTC CACTTACCATGTTACGAC 62.5 36.8 51.1 27.7 12 8 GG 3850 0 0.985 3817 0 0.985 2649 0.694 35 121 55.51
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
- Primer ID : 11
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
| Primer | sequence | tm max | tm min | GC count |
|
||||||
|
|---------|--------------------|--------|--------|----------|
|
||||||
|
| Forward | ACACCGCCCGTCACTCTC | 62.5 | 36.8 | 12 |
|
||||||
|
| Reverse | CCAAGTGCACCTTCCGGT | 60.7 | 28.9 | 11 |
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
- amplifying 3837/3909 sequences\
|
||||||
|
- identify 2650/3876 Species
|
||||||
|
- Size ranging from 54bp to 140bp (mean: 74.75 bp)
|
||||||
|
|
||||||
|
## Testing the new primer pair
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obipcr --forward ACACCGCCCGTCACTCTC \
|
||||||
|
--reverse CCAAGTGCACCTTCCGGT \
|
||||||
|
-e 5 \
|
||||||
|
-l 30 -L 150 \
|
||||||
|
-c \
|
||||||
|
mito.vert.fasta \
|
||||||
|
> Teleostei_11.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
head Teleostei_11.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
>NC_022183_sub[925..998] {"count":1,"definition":"Acrossocheilus hemispinus mitochondrion, complete genome.","direction":"forward","forward_error":1,"forward_match":"acaccgcccgtcaccctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:356810 [Acrossocheilus hemispinus]@species","reverse_error":0,"reverse_match":"ccaagtgcaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Acrossocheilus hemispinus","species_name":"Acrossocheilus hemispinus","species_taxid":"taxon:356810 [Acrossocheilus hemispinus]@species","taxid":"taxon:356810 [Acrossocheilus hemispinus]@species"}
|
||||||
|
cccgtcaaaatacaccaaaaatacttaatacaataacactaacaaggggaggcaagtcgt
|
||||||
|
aacatggtaagtgt
|
||||||
|
>NC_018560_sub[916..988] {"count":1,"definition":"Astatotilapia calliptera mitochondrion, complete genome.","direction":"forward","forward_error":0,"forward_match":"acaccgcccgtcactctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:8154 [Astatotilapia calliptera]@species","reverse_error":1,"reverse_match":"ccaagtacaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Astatotilapia calliptera (eastern happy)","species_name":"Astatotilapia calliptera","species_taxid":"taxon:8154 [Astatotilapia calliptera]@species","taxid":"taxon:8154 [Astatotilapia calliptera]@species"}
|
||||||
|
cccaagccaacaacatcctataaataatacattttaccggtaaaggggaggcaagtcgta
|
||||||
|
acatggtaagtgt
|
||||||
|
>NC_056117_sub[923..997] {"count":1,"definition":"Pseudocrossocheilus tridentis mitochondrion, complete genome.","direction":"forward","forward_error":0,"forward_match":"acaccgcccgtcactctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species","reverse_error":0,"reverse_match":"ccaagtgcaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Pseudocrossocheilus tridentis","species_name":"Pseudocrossocheilus tridentis","species_taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species","taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species"}
|
||||||
|
ccctgtcaaaaagcatcaaatatatataataaattagcaatgacaaggggaggcaagtcg
|
||||||
|
taacacggtaagtgt
|
||||||
|
>NC_045904_sub[919..997] {"count":1,"definition":"Eospalax fontanierii mitochondrion, complete genome.","direction":"forward","forward_error":1,"forward_match":"acaccgcccgtcgctctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:146134 [Eospalax fontanierii]@species","reverse_error":4,"reverse_match":"ccaagcacactttccagt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Eospalax fontanierii","species_name":"Eospalax fontanierii","species_taxid":"taxon:146134 [Eospalax fontanierii]@species","taxid":"taxon:146134 [Eospalax fontanierii]@species"}
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
convert the fasta file to csv
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obicsv --auto -s -i Teleostei_11.fasta > Teleostei_11.csv
|
||||||
|
```
|
||||||
|
|
||||||
|
and display the begining of the table
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
head Teleostei_11.csv | csvlook
|
||||||
|
```
|
||||||
|
|
||||||
|
``` csv
|
||||||
|
| id | count | direction | forward_error | forward_match | forward_primer | ori_taxid | reverse_error | reverse_match | reverse_primer | scientific_name | species_name | species_taxid | taxid | sequence |
|
||||||
|
| ------------------------- | ----- | --------- | ------------- | ------------------ | ------------------ | ---------------------------------------------------- | ------------- | ------------------ | ------------------ | ------------------------------------------------------ | ----------------------------- | ---------------------------------------------------- | ---------------------------------------------------- | ------------------------------------------------------------------------------- |
|
||||||
|
| NC_022183_sub[925..998] | True | forward | True | acaccgcccgtcaccctc | ACACCGCCCGTCACTCTC | taxon:356810 [Acrossocheilus hemispinus]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Acrossocheilus hemispinus | Acrossocheilus hemispinus | taxon:356810 [Acrossocheilus hemispinus]@species | taxon:356810 [Acrossocheilus hemispinus]@species | cccgtcaaaatacaccaaaaatacttaatacaataacactaacaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_018560_sub[916..988] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:8154 [Astatotilapia calliptera]@species | 1 | ccaagtacaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Astatotilapia calliptera (eastern happy) | Astatotilapia calliptera | taxon:8154 [Astatotilapia calliptera]@species | taxon:8154 [Astatotilapia calliptera]@species | cccaagccaacaacatcctataaataatacattttaccggtaaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_056117_sub[923..997] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:887881 [Pseudocrossocheilus tridentis]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Pseudocrossocheilus tridentis | Pseudocrossocheilus tridentis | taxon:887881 [Pseudocrossocheilus tridentis]@species | taxon:887881 [Pseudocrossocheilus tridentis]@species | ccctgtcaaaaagcatcaaatatatataataaattagcaatgacaaggggaggcaagtcgtaacacggtaagtgt |
|
||||||
|
| NC_045904_sub[919..997] | True | forward | True | acaccgcccgtcgctctc | ACACCGCCCGTCACTCTC | taxon:146134 [Eospalax fontanierii]@species | 4 | ccaagcacactttccagt | CCAAGTGCACCTTCCGGT | mitochondrion Eospalax fontanierii | Eospalax fontanierii | taxon:146134 [Eospalax fontanierii]@species | taxon:146134 [Eospalax fontanierii]@species | ctcaagtacataaacttggatatattcttaataacccaacaaaaatattagaggagataagtcgtaacaaggtaagcat |
|
||||||
|
| NC_018546_sub[916..987] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:30732 [Oryzias melastigma]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Oryzias melastigma (Indian medaka) | Oryzias melastigma | taxon:30732 [Oryzias melastigma]@species | taxon:30732 [Oryzias melastigma]@species | cccgacccattttaaaaattaaataaaagatttcaggaactaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_044151_sub[922..993] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:2597641 [Sicyopterus squamosissimus]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Sicyopterus squamosissimus (cling goby) | Sicyopterus squamosissimus | taxon:2597641 [Sicyopterus squamosissimus]@species | taxon:2597641 [Sicyopterus squamosissimus]@species | cccaaaacaaacacacacataaataagaaaaaatgaaaataaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_044152_sub[922..994] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:2597642 [Sicyopterus stiphodonoides]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Sicyopterus stiphodonoides (cling goby) | Sicyopterus stiphodonoides | taxon:2597642 [Sicyopterus stiphodonoides]@species | taxon:2597642 [Sicyopterus stiphodonoides]@species | cccaaaacaaacacacacataaataagaaaaaantgaaaataaaggggaggcaagtcgtaacatggtaagtgt |
|
||||||
|
| NC_026976_sub[1453..1531] | True | forward | True | acaccgcccgtcactccc | ACACCGCCCGTCACTCTC | taxon:9545 [Macaca nemestrina]@species | 1 | ccaagtgcaccttccagt | CCAAGTGCACCTTCCGGT | mitochondrion Macaca nemestrina (pig-tailed macaque) | Macaca nemestrina | taxon:9545 [Macaca nemestrina]@species | taxon:9545 [Macaca nemestrina]@species | ctcaaatatatttaaggaacatcttaactaaacgccctaatatttatatagaggggataagtcgtaacatggtaagtgt |
|
||||||
|
| NC_031553_sub[921..995] | True | forward | False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:643337 [Puntioplites proctozystron]@species | 0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Puntioplites proctozystron | Puntioplites proctozystron | taxon:643337 [Puntioplites proctozystron]@species | taxon:643337 [Puntioplites proctozystron]@species | ccctgtcaaaacgcactaaaaatatctaatacaaaagcaccgacaaggggaggcaagtcgtaacacggtaagtgt |
|
||||||
|
```
|
||||||
|
|
||||||
|
# We are now switching to R
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Preparing our R session
|
||||||
|
|
||||||
|
First we have to download the two follong libraries
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
library(tidyverse)
|
||||||
|
library(ggpubr)
|
||||||
|
library(ROBITools4)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Loading the data
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
|
||||||
|
fish <- read_csv('Teleostei_11.csv', show_col_types = FALSE)
|
||||||
|
taxo <- read_ncbi_taxdump('ncbitaxo_20250211')
|
||||||
|
assign_default_taxonomy(taxo)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
Looking for Teleostei taxid
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
teleo_taxid <- ecofind('Teleostei')
|
||||||
|
teleo_taxid
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Format taxids
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
fish %>% mutate(
|
||||||
|
taxid = as_taxid(
|
||||||
|
as.integer(
|
||||||
|
str_split_fixed(
|
||||||
|
str_split_fixed(
|
||||||
|
taxid,pattern = " ",
|
||||||
|
n = 2)[,1],
|
||||||
|
":",
|
||||||
|
2)[,2]))
|
||||||
|
) %>%
|
||||||
|
as_tbl_obipcr() %>%
|
||||||
|
mutate(across(taxon(),
|
||||||
|
.names="category",
|
||||||
|
.fn=taxonomy_classifier(Teleostei = 32443))) %>%
|
||||||
|
group_by(category) %>%
|
||||||
|
mutate(weight = taxonomic_weights(taxid,taxo)) %>%
|
||||||
|
ungroup() -> fish
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## The fish tibble
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
head(fish,n = 4)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Identifying which sequences belongs fish
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
table(fish$category)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Testing the conservation of the priming sites
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward <- pssm(fish$forward_match,
|
||||||
|
weights = fish$weight,
|
||||||
|
categories = fish$category)
|
||||||
|
|
||||||
|
pssm_reverse <- pssm(fish$reverse_match,
|
||||||
|
weights = fish$weight,
|
||||||
|
categories = fish$category)
|
||||||
|
```
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Rescaling the matrix as Shanon entropy
|
||||||
|
|
||||||
|
$$
|
||||||
|
H = - \sum_{i \in \{A,C,G,T\}} p_i \times \frac{\log(p_i)}{\log(2)}
|
||||||
|
$$
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward <- pssm_scale_shanon(pssm_forward)
|
||||||
|
pssm_reverse <- pssm_scale_shanon(pssm_reverse)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Display the rescaled matrix
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## The DNA logo of our primer pair
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
flogo <- ggbarcodelogo(pssm_forward) +
|
||||||
|
xlab("Forward primer") + ylab("Bits")
|
||||||
|
rlogo <- ggbarcodelogo(pssm_reverse) +
|
||||||
|
xlab("Reverse primer") + ylab("Bits")
|
||||||
|
|
||||||
|
ggarrange(flogo,rlogo,ncol=2) -> dnaplot
|
||||||
|
|
||||||
|
dnaplot
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## How many mismatches ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
ggbarcodemistmatch(fish$forward_error,
|
||||||
|
fish$reverse_error,
|
||||||
|
otu=fish$species_name,
|
||||||
|
categories=fish$category) + theme_minimal()
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Are we discriminate taxa ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
with(fish %>% filter(category == "Teleostei"),
|
||||||
|
discriminated_at_rank(taxid,
|
||||||
|
c("species","genus","family","order"),
|
||||||
|
sequence))
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## How many sequences will provide information at rank ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
with(fish %>% filter(category == "Teleostei"),
|
||||||
|
discriminant_at_rank(taxid,
|
||||||
|
c("species","genus","family","order"),
|
||||||
|
sequence))
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Is it the same for *Cyprinidae* ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
cyprinidae_taxid <- ecofind('Cyprinidae')
|
||||||
|
cyprinidae_taxid
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Classify according to both categories
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
fish %>%
|
||||||
|
mutate(across(taxon(),
|
||||||
|
.names="category2",
|
||||||
|
.fn=taxonomy_classifier(Teleostei = 32443,
|
||||||
|
Cyprinidae = 7953))) -> fish
|
||||||
|
|
||||||
|
table(fish$category2)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Are we discriminate taxa ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
with(fish %>% filter(category2 == "Cyprinidae"),
|
||||||
|
discriminated_at_rank(taxid,
|
||||||
|
c("species","genus"),
|
||||||
|
sequence))
|
||||||
|
```
|
||||||
|
|
||||||
|
# Go back to unix
|
||||||
|
|
||||||
|
## We run ecoPrimers and ecoPCR on the select primer pair
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
ecoPrimers -d vertebrata \
|
||||||
|
-e 3 -3 2 \
|
||||||
|
-l 30 -L 150 \
|
||||||
|
-r 7953 -c > Cyprinidae.ecoprimers
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obipcr --forward ACGGCGTAAAGGGTGGTT \
|
||||||
|
--reverse TATCTAATCCCAGTTTGT \
|
||||||
|
-e 5 \
|
||||||
|
-l 30 -L 500 \
|
||||||
|
-c \
|
||||||
|
mito.vert.fasta \
|
||||||
|
> Cyprinidae_14.fasta
|
||||||
|
```
|
||||||
|
|
||||||
|
```{bash}
|
||||||
|
#| eval: false
|
||||||
|
#| echo: true
|
||||||
|
obicsv --auto -s -i Cyprinidae_14.fasta > Cyprinidae_14.csv
|
||||||
|
```
|
||||||
|
|
||||||
|
# Go back to R
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
cyprinidae <- read_csv('Cyprinidae_14.csv',
|
||||||
|
show_col_types = FALSE) %>%
|
||||||
|
mutate(
|
||||||
|
taxid = as_taxid(
|
||||||
|
as.integer(
|
||||||
|
str_split_fixed(
|
||||||
|
str_split_fixed(
|
||||||
|
taxid,pattern = " ",
|
||||||
|
n = 2)[,1],
|
||||||
|
":",
|
||||||
|
2)[,2]))
|
||||||
|
) %>%
|
||||||
|
as_tbl_obipcr() %>%
|
||||||
|
mutate(across(taxon(),
|
||||||
|
.names="category",
|
||||||
|
.fn=taxonomy_classifier(Teleostei = 32443,
|
||||||
|
Cyprinidae = 7953))) %>%
|
||||||
|
group_by(category) %>%
|
||||||
|
mutate(weight = taxonomic_weights(taxid,taxo)) %>%
|
||||||
|
ungroup()
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Identifying which sequences belongs fish and *Cyprinidae*
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
table(cyprinidae$category)
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Looking for conservation
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
pssm_forward <- pssm(cyprinidae$forward_match,
|
||||||
|
weights = cyprinidae$weight,
|
||||||
|
categories = cyprinidae$category) %>%
|
||||||
|
pssm_scale_shanon()
|
||||||
|
|
||||||
|
pssm_reverse <- pssm(cyprinidae$reverse_match,
|
||||||
|
weights = cyprinidae$weight,
|
||||||
|
categories = cyprinidae$category) %>%
|
||||||
|
pssm_scale_shanon()
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Plot the new DNA logo
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
flogo <- ggbarcodelogo(pssm_forward) +
|
||||||
|
xlab("Forward primer") + ylab("Bits")
|
||||||
|
rlogo <- ggbarcodelogo(pssm_reverse) +
|
||||||
|
xlab("Reverse primer") + ylab("Bits")
|
||||||
|
|
||||||
|
ggarrange(flogo,rlogo,ncol=2) -> dnaplot
|
||||||
|
|
||||||
|
dnaplot
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## How many mismatches ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
ggbarcodemistmatch(cyprinidae$forward_error,
|
||||||
|
cyprinidae$reverse_error,
|
||||||
|
otu=cyprinidae$species_name,
|
||||||
|
categories=cyprinidae$category) + theme_minimal()
|
||||||
|
```
|
||||||
|
|
||||||
|
------------------------------------------------------------------------
|
||||||
|
|
||||||
|
## Are we discriminate *Cyprinidae* taxa ?
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
#| echo: true
|
||||||
|
with(cyprinidae %>% filter(category == "Cyprinidae"),
|
||||||
|
discriminated_at_rank(taxid,
|
||||||
|
c("species","genus"),
|
||||||
|
sequence))
|
||||||
|
```
|
||||||
1227
jupyterhub_volumes/course/biodiversity_metrics_exercises.ipynb
Normal file
1227
jupyterhub_volumes/course/biodiversity_metrics_exercises.ipynb
Normal file
File diff suppressed because it is too large
Load Diff
@@ -2,128 +2,883 @@
|
|||||||
"cells": [
|
"cells": [
|
||||||
{
|
{
|
||||||
"cell_type": "markdown",
|
"cell_type": "markdown",
|
||||||
|
"id": "30438c30",
|
||||||
"metadata": {},
|
"metadata": {},
|
||||||
"source": [
|
"source": [
|
||||||
"# Unix Essentials — Bash Exercises\n",
|
"# Unix Essentials — Bash Practice Notebook\n",
|
||||||
"\n",
|
"\n",
|
||||||
"This notebook contains short hands-on Bash exercises.\n",
|
"This notebook contains 50 small Bash exercises grouped by topic.\n",
|
||||||
"Each exercise has a hidden solution that can be unfolded when needed."
|
"Each exercise includes a hidden solution that can be revealed in Jupyter."
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "markdown",
|
"cell_type": "markdown",
|
||||||
|
"id": "39d711f9",
|
||||||
"metadata": {},
|
"metadata": {},
|
||||||
"source": [
|
"source": [
|
||||||
"## Exercise 1 – Listing and Filtering Files\n",
|
"## Series 1 — Paths and Directories"
|
||||||
"\n",
|
]
|
||||||
"Create three files and list only those whose name ends with `.log`."
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "6fb7335e",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 1.1 — Show your current working directory"
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "code",
|
"cell_type": "code",
|
||||||
"execution_count": null,
|
"execution_count": null,
|
||||||
|
"id": "2b8575f3",
|
||||||
"metadata": {},
|
"metadata": {},
|
||||||
"outputs": [],
|
"outputs": [],
|
||||||
"source": [
|
"source": [
|
||||||
"# your work here\n",
|
"# your work here\n",
|
||||||
"touch report.log notes.txt errors.log\n",
|
"pwd"
|
||||||
"# list files ending with .log"
|
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "code",
|
"cell_type": "code",
|
||||||
"execution_count": null,
|
"execution_count": null,
|
||||||
|
"id": "21f63bb0",
|
||||||
"metadata": {
|
"metadata": {
|
||||||
"jupyter": {
|
"jupyter": {
|
||||||
"source_hidden": true,
|
"outputs_hidden": true,
|
||||||
"outputs_hidden": true
|
"source_hidden": true
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"outputs": [],
|
"outputs": [],
|
||||||
"source": [
|
"source": [
|
||||||
"# Solution\n",
|
"# Solution\n",
|
||||||
"ls *.log"
|
"pwd"
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "markdown",
|
"cell_type": "markdown",
|
||||||
|
"id": "61a624bf",
|
||||||
"metadata": {},
|
"metadata": {},
|
||||||
"source": [
|
"source": [
|
||||||
"## Exercise 2 – Redirecting Output\n",
|
"### Exercise 1.2 — Create a new directory named `testdir`"
|
||||||
"\n",
|
|
||||||
"List the `/etc` directory and save the results in a file named `listing.txt`, then display the first five lines of that file."
|
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "code",
|
"cell_type": "code",
|
||||||
"execution_count": null,
|
"execution_count": null,
|
||||||
|
"id": "4a4df387",
|
||||||
"metadata": {},
|
"metadata": {},
|
||||||
"outputs": [],
|
"outputs": [],
|
||||||
"source": [
|
"source": [
|
||||||
"# your work here\n",
|
"# your work here\n",
|
||||||
"# 1. list /etc\n",
|
"mkdir testdir"
|
||||||
"# 2. redirect output to listing.txt\n",
|
|
||||||
"# 3. show first five lines"
|
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "code",
|
"cell_type": "code",
|
||||||
"execution_count": null,
|
"execution_count": null,
|
||||||
|
"id": "2b5cfbca",
|
||||||
"metadata": {
|
"metadata": {
|
||||||
"jupyter": {
|
"jupyter": {
|
||||||
"source_hidden": true,
|
"outputs_hidden": true,
|
||||||
"outputs_hidden": true
|
"source_hidden": true
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"outputs": [],
|
"outputs": [],
|
||||||
"source": [
|
"source": [
|
||||||
"# Solution\n",
|
"# Solution\n",
|
||||||
"ls /etc > listing.txt\n",
|
"mkdir testdir"
|
||||||
"head -5 listing.txt"
|
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "markdown",
|
"cell_type": "markdown",
|
||||||
|
"id": "2dccbb61",
|
||||||
"metadata": {},
|
"metadata": {},
|
||||||
"source": [
|
"source": [
|
||||||
"## Exercise 3 – Using a For Loop\n",
|
"### Exercise 1.3 — Move into `testdir` using a relative path"
|
||||||
"\n",
|
|
||||||
"Write a loop that prints the line count of each `.txt` file in the current directory."
|
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "code",
|
"cell_type": "code",
|
||||||
"execution_count": null,
|
"execution_count": null,
|
||||||
|
"id": "fb73ca3c",
|
||||||
"metadata": {},
|
"metadata": {},
|
||||||
"outputs": [],
|
"outputs": [],
|
||||||
"source": [
|
"source": [
|
||||||
"# your work here\n",
|
"# your work here\n",
|
||||||
"# hint: use wc -l"
|
"cd testdir"
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "code",
|
"cell_type": "code",
|
||||||
"execution_count": null,
|
"execution_count": null,
|
||||||
|
"id": "ba670a20",
|
||||||
"metadata": {
|
"metadata": {
|
||||||
"jupyter": {
|
"jupyter": {
|
||||||
"source_hidden": true,
|
"outputs_hidden": true,
|
||||||
"outputs_hidden": true
|
"source_hidden": true
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"outputs": [],
|
"outputs": [],
|
||||||
"source": [
|
"source": [
|
||||||
"# Solution\n",
|
"# Solution\n",
|
||||||
"for f in *.txt; do\n",
|
"cd testdir"
|
||||||
" echo \"$f: $(wc -l < \"$f\") lines\"\n",
|
|
||||||
"done"
|
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
"cell_type": "markdown",
|
"cell_type": "markdown",
|
||||||
|
"id": "4f7e5817",
|
||||||
"metadata": {},
|
"metadata": {},
|
||||||
"source": [
|
"source": [
|
||||||
"---\n",
|
"### Exercise 1.4 — Create two subdirectories `a` and `b` in one command"
|
||||||
"All solutions are hidden by default (`source_hidden: true`). Students can unfold them in Jupyter’s interface to compare with their own answers."
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "30be8f44",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# your work here\n",
|
||||||
|
"mkdir a b"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "caf92714",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"mkdir a b"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "edec9041",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 1.5 — Return to the parent directory using `..`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "32a0f1df",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# your work here\n",
|
||||||
|
"cd .."
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "2a0aa92f",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"cd .."
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "31917159",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 1.6 — Create nested directories `one/two/three` in a single command"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "c0a313c3",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# your work here\n",
|
||||||
|
"mkdir -p one/two/three"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "4af63dce",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"mkdir -p one/two/three"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "24ee949e",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 1.7 — List the absolute path of the current directory"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "8258fff7",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# your work here\n",
|
||||||
|
"pwd"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "a6a062b2",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"pwd"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "6d724d3e",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 1.8 — Create a directory using an absolute path"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "5f497f7c",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# your work here\n",
|
||||||
|
"mkdir /tmp/mydir"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "1d1d4e27",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"mkdir /tmp/mydir"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "0a4cbe5b",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 1.9 — Display both `.` and `..` directories with `ls -a`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "7d962a9f",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# your work here\n",
|
||||||
|
"ls -a"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "91994de2",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"ls -a"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "e147ff34",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 1.10 — Remove the directory `/tmp/mydir`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "dcae28e3",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# your work here\n",
|
||||||
|
"rmdir /tmp/mydir"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "1a000f14",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"rmdir /tmp/mydir"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "578548f7",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"## Series 2 — File Manipulation"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "813140d5",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 2.1 — Create an empty file named `notes.txt`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "08385872",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"touch notes.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "a474ad37",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"touch notes.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "6e918f3d",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 2.2 — Copy `notes.txt` to `backup.txt`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "faf85985",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"cp notes.txt backup.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "4d3e54d5",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"cp notes.txt backup.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "2c924f2e",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 2.3 — Rename `backup.txt` to `archive.txt`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "2d4adeb4",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"mv backup.txt archive.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "2c62e70f",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"mv backup.txt archive.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "c9e525a7",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 2.4 — Create 3 files and remove one with `rm`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "3ef53a3a",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"touch a.txt b.txt c.txt\n",
|
||||||
|
"rm b.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "55e07074",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"touch a.txt b.txt c.txt\n",
|
||||||
|
"rm b.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "b5a406b4",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 2.5 — Remove a directory recursively"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "2c819a49",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"mkdir -p tmpdir/sub\n",
|
||||||
|
"rm -rf tmpdir"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "b958a668",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"mkdir -p tmpdir/sub\n",
|
||||||
|
"rm -rf tmpdir"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "9aa4996e",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"## Series 3 — Redirections and Pipes"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "ada90797",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 3.1 — Save the output of `ls` to a file `list.txt`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "25afa75b",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"ls > list.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "80ca4767",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"ls > list.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "61c3bff6",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 3.2 — Append the date to `list.txt`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "b7849f15",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"date >> list.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "83b08fe6",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"date >> list.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "600edcaa",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 3.3 — Count lines of `list.txt` with a pipe"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "37e859f4",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"cat list.txt | wc -l"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "d1429a1c",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"cat list.txt | wc -l"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "a901cf34",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 3.4 — Redirect error messages to a file"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "f2c1d530",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"ls /fakepath 2> errors.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "66c68bc4",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"ls /fakepath 2> errors.txt"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "72e5eca4",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"## Series 4 — Viewing Results"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "dd7cbf2e",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 4.1 — Display the first 5 lines of `/etc/passwd`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "195c0f25",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"head -5 /etc/passwd"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "72dc0297",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"head -5 /etc/passwd"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "227ebdf8",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 4.2 — Show the last 3 lines of `/etc/passwd`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "3a829074",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"tail -3 /etc/passwd"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "e66f1752",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"tail -3 /etc/passwd"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "826cbb41",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 4.3 — Use `grep` to show lines containing 'root'"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "df9a877b",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"grep root /etc/passwd"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "5ed43d3d",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"grep root /etc/passwd"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "a6c2f0a8",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"## Series 5 — Process Management"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "333ab7c1",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 5.1 — List current processes"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "41dc9dfb",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"ps"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "c0f28455",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"ps"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "markdown",
|
||||||
|
"id": "c2d37e8f",
|
||||||
|
"metadata": {},
|
||||||
|
"source": [
|
||||||
|
"### Exercise 5.2 — Display dynamic process list with `top`"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "7931c9aa",
|
||||||
|
"metadata": {},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"top"
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"cell_type": "code",
|
||||||
|
"execution_count": null,
|
||||||
|
"id": "947570cf",
|
||||||
|
"metadata": {
|
||||||
|
"jupyter": {
|
||||||
|
"outputs_hidden": true,
|
||||||
|
"source_hidden": true
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"outputs": [],
|
||||||
|
"source": [
|
||||||
|
"# Solution\n",
|
||||||
|
"top"
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
],
|
],
|
||||||
|
|||||||
1560
jupyterhub_volumes/course/unix_exercises_bash.ipynb
Normal file
1560
jupyterhub_volumes/course/unix_exercises_bash.ipynb
Normal file
File diff suppressed because it is too large
Load Diff
File diff suppressed because one or more lines are too long
@@ -2,9 +2,11 @@
|
|||||||
title: "Regular Expressions"
|
title: "Regular Expressions"
|
||||||
format:
|
format:
|
||||||
revealjs:
|
revealjs:
|
||||||
theme: beige # thème des slides
|
|
||||||
css: ../../slides.css
|
css: ../../slides.css
|
||||||
transition: fade # effet de transition entre les slides
|
transition: slide
|
||||||
|
scrollable: true
|
||||||
|
theme: beige
|
||||||
|
html-math-method: mathjax
|
||||||
---
|
---
|
||||||
|
|
||||||
|
|
||||||
|
Before Width: | Height: | Size: 9.6 KiB After Width: | Height: | Size: 9.6 KiB |
|
Before Width: | Height: | Size: 6.5 KiB After Width: | Height: | Size: 6.5 KiB |
|
Before Width: | Height: | Size: 146 KiB After Width: | Height: | Size: 146 KiB |
|
Before Width: | Height: | Size: 110 KiB After Width: | Height: | Size: 110 KiB |
|
Before Width: | Height: | Size: 2.5 KiB After Width: | Height: | Size: 2.5 KiB |
|
Before Width: | Height: | Size: 15 KiB After Width: | Height: | Size: 15 KiB |
|
Before Width: | Height: | Size: 15 KiB After Width: | Height: | Size: 15 KiB |
|
Before Width: | Height: | Size: 10 KiB After Width: | Height: | Size: 10 KiB |
|
Before Width: | Height: | Size: 13 KiB After Width: | Height: | Size: 13 KiB |
|
Before Width: | Height: | Size: 155 KiB After Width: | Height: | Size: 155 KiB |
|
Before Width: | Height: | Size: 15 KiB After Width: | Height: | Size: 15 KiB |
|
Before Width: | Height: | Size: 54 KiB After Width: | Height: | Size: 54 KiB |
|
Before Width: | Height: | Size: 29 KiB After Width: | Height: | Size: 29 KiB |
|
Before Width: | Height: | Size: 31 KiB After Width: | Height: | Size: 31 KiB |
|
Before Width: | Height: | Size: 23 KiB After Width: | Height: | Size: 23 KiB |
|
Before Width: | Height: | Size: 31 KiB After Width: | Height: | Size: 31 KiB |
|
Before Width: | Height: | Size: 4.6 KiB After Width: | Height: | Size: 4.6 KiB |
|
Before Width: | Height: | Size: 3.4 KiB After Width: | Height: | Size: 3.4 KiB |
|
Before Width: | Height: | Size: 2.9 KiB After Width: | Height: | Size: 2.9 KiB |
|
Before Width: | Height: | Size: 4.0 KiB After Width: | Height: | Size: 4.0 KiB |
|
Before Width: | Height: | Size: 4.4 KiB After Width: | Height: | Size: 4.4 KiB |
|
Before Width: | Height: | Size: 4.5 KiB After Width: | Height: | Size: 4.5 KiB |
|
Before Width: | Height: | Size: 4.5 KiB After Width: | Height: | Size: 4.5 KiB |
|
Before Width: | Height: | Size: 265 KiB After Width: | Height: | Size: 265 KiB |
|
Before Width: | Height: | Size: 198 KiB After Width: | Height: | Size: 198 KiB |
|
Before Width: | Height: | Size: 231 KiB After Width: | Height: | Size: 231 KiB |
|
Before Width: | Height: | Size: 18 KiB After Width: | Height: | Size: 18 KiB |
|
Before Width: | Height: | Size: 32 KiB After Width: | Height: | Size: 32 KiB |
|
Before Width: | Height: | Size: 5.3 KiB After Width: | Height: | Size: 5.3 KiB |
|
Before Width: | Height: | Size: 86 KiB After Width: | Height: | Size: 86 KiB |
|
Before Width: | Height: | Size: 13 KiB After Width: | Height: | Size: 13 KiB |
|
Before Width: | Height: | Size: 10 KiB After Width: | Height: | Size: 10 KiB |
|
Before Width: | Height: | Size: 13 KiB After Width: | Height: | Size: 13 KiB |
|
Before Width: | Height: | Size: 22 KiB After Width: | Height: | Size: 22 KiB |
|
Before Width: | Height: | Size: 4.4 KiB After Width: | Height: | Size: 4.4 KiB |
|
Before Width: | Height: | Size: 12 KiB After Width: | Height: | Size: 12 KiB |
@@ -6,12 +6,11 @@ title: |
|
|||||||
author: frederic.boyer@univ-grenoble-alpes.fr
|
author: frederic.boyer@univ-grenoble-alpes.fr
|
||||||
format:
|
format:
|
||||||
revealjs:
|
revealjs:
|
||||||
theme: beige
|
|
||||||
css: ../../slides.css
|
css: ../../slides.css
|
||||||
transition: fade
|
transition: slide
|
||||||
width: 1280
|
scrollable: true
|
||||||
height: 720
|
theme: beige
|
||||||
center: true
|
html-math-method: mathjax
|
||||||
---
|
---
|
||||||
|
|
||||||
# Introduction to Unix
|
# Introduction to Unix
|
||||||
1248
web_src/05_Lectures/05_Metabarcoding/Biodiversity_indices/Slides.qmd
Normal file
1248
web_src/05_Lectures/05_Metabarcoding/Biodiversity_indices/Slides.qmd
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,167 @@
|
|||||||
|
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||||
|
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
|
||||||
|
<svg width="100%" height="100%" viewBox="0 0 2031 2071" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xml:space="preserve" style="fill-rule:evenodd;clip-rule:evenodd;stroke-linecap:square;stroke-linejoin:round;stroke-miterlimit:1.41421;">
|
||||||
|
<g transform="matrix(1,0,0,1,-192,-982)">
|
||||||
|
<g id="Main-Plot">
|
||||||
|
<g>
|
||||||
|
<g id="Grille">
|
||||||
|
<g transform="matrix(1.1808,0,0,1,-75.4118,0)">
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,-172.262)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,975.279)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,811.344)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,647.41)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,1303.15)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,319.541)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,155.607)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,-8.32717)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,1139.21)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,483.476)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(3.34494e-16,1.1808,-1,2.83277e-16,3205.71,544.557)">
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,-172.262)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,975.279)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,811.344)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
|
||||||
|
</g>
|
||||||
|
<g transform="matrix(1,0,0,1.31073,-19.234,647.41)">
|
||||||
|
<path d="M436.328,1027.97L1919.68,1027.97" style="fill:none;stroke-width:50.1px;stroke:rgb(181,181,181);"/>
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%% This BibTeX bibliography file was created using BibDesk.
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%% http://bibdesk.sourceforge.net/
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%% Created for Eric Coissac at 2018-10-18 14:52:51 +0200
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%% Saved with string encoding Unicode (UTF-8)
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@article{Tsallis:94:00,
|
||||||
|
Author = {Tsallis, Constantino},
|
||||||
|
Date-Added = {2018-10-18 14:52:41 +0200},
|
||||||
|
Date-Modified = {2018-10-18 14:52:49 +0200},
|
||||||
|
Journal = {Quim. Nova},
|
||||||
|
Number = 6,
|
||||||
|
Pages = {468--471},
|
||||||
|
Title = {What are the numbers that experiments provide},
|
||||||
|
Volume = 17,
|
||||||
|
Year = 1994}
|
||||||
|
|
||||||
|
|
||||||
|
@ARTICLE{Whittaker:10:00,
|
||||||
|
title = "Meta-analyses and mega-mistakes: calling time on meta-analysis
|
||||||
|
of the species richness-productivity relationship",
|
||||||
|
author = "Whittaker, Robert J",
|
||||||
|
abstract = "The form of the species richness-productivity relationship
|
||||||
|
(SRPR) is both theoretically important and contentious. In an
|
||||||
|
effort to distill general patterns, ecologists have undertaken
|
||||||
|
meta-analyses, within which each SRPR data set is first
|
||||||
|
classified into one of five alternative forms: positive, humped
|
||||||
|
(unimodal), negative, U-shaped (unimodal), and no relationship.
|
||||||
|
Herein, I first provide a critique of this approach, based on 68
|
||||||
|
plant data sets/ studies used in three meta-analyses published
|
||||||
|
in Ecology. The meta-analyses are shown to have resulted in
|
||||||
|
highly divergent outcomes, inconsistent and often highly
|
||||||
|
inappropriate classification of data sets, and the introduction
|
||||||
|
and multiplication of errors from one meta-analysis to the next.
|
||||||
|
I therefore call on the ecological community at large to adopt a
|
||||||
|
far more rigorous and critical attitude to the use of
|
||||||
|
meta-analysis. Second, I develop the argument that the
|
||||||
|
literature on the SRPR continues to be bedeviled by a common
|
||||||
|
failing to appreciate the fundamental importance of the scale of
|
||||||
|
analysis, beginning with the confusion evident between concepts
|
||||||
|
of grain, focus, and extent. I postulate that variation in the
|
||||||
|
form of the SRPR at fine scales of analysis owes much to
|
||||||
|
artifacts of the sampling regime adopted. An improved
|
||||||
|
understanding may emerge from combining sampling theory with an
|
||||||
|
understanding of the factors controlling the form of species
|
||||||
|
abundance distributions and species accumulation curves.",
|
||||||
|
journal = "Ecology",
|
||||||
|
publisher = "Eco Soc America",
|
||||||
|
volume = 91,
|
||||||
|
number = 9,
|
||||||
|
pages = "2522--2533",
|
||||||
|
month = sep,
|
||||||
|
year = 2010
|
||||||
|
}
|
||||||
|
|
||||||
Reference in New Issue
Block a user