Replace Accesion Headers by full ncbi Lineage Taxnomy
Hi everybody
I have several multifasta files with headers like this:
>NC_014760.1:c365195-363993 Mycoplasma bovis PG45 clone MU clone A2, complete genome
>NC_013511.1:c476217-475021 Mycoplasma hominis ATCC 23114 chromosome complete genome
I would like to replace this headers by ncbi full taxonomy:
>Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,Bacillus anthracis
Can you help me with that?
This question FASTA file with taxid, want to obtain lineage and put into header is almost the same that I have, but in there the user had ncbi tax ID instead of accesion number-
Thank you
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shenwei356
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dllopezr •
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dllopezr •
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Dataset and tools:
- Genank accession -> taxid : nucl_gb.accession2taxid.gz
- Taxid -> Lineage: taxonkit lineage
- Replacing fasta header with corresponding replacements: seqkit replace
Here we go:
Few lines of nucl_gb.accession2taxid.gz
$ zcat nucl_gb.accession2taxid.gz | head -n 3 | column -t accession accession.version taxid gi A00002 A00002.1 9913 2 A00003 A00003.1 9913 3Retrieving the accession from fasta file
$ cat seqs.fa >NC_014760.1:c365195-363993 Mycoplasma bovis PG45 clone MU clone A2, complete genome actg >NC_013511.1:c476217-475021 Mycoplasma hominis ATCC 23114 chromosome complete genome ACTN $ seqkit seq -n -i --id-regexp '^(.+):' seqs.fa | tee seqs.fa.id NC_014760.1 NC_013511.1Searching the taxids
$ time csvtk grep -t -f accession.version -P seqs.fa.id nucl_gb.accession2taxid.gz \ | csvtk cut -t -f accession.version,taxid | tee seqs.fa.id2taxid NC_013511.1 347256 NC_014760.1 289397 real 0m50.546s user 1m44.892s sys 0m4.160s # faster using shell grep, $ time zcat nucl_gb.accession2taxid.gz \ | grep -w -f seqs.fa.id | cut -f 2,3 | tee seqs.fa.id2taxid NC_013511.1 347256 NC_014760.1 289397 real 0m19.034s user 0m23.868s sys 0m1.384sComputing lineage
$ time cat seqs.fa.id2taxid \ | taxonkit lineage -i 2 \ | sed 1d | cut -f 1,3 | tee seqs.fa.id2taxid2lineage NC_013511.1 cellular organisms;Bacteria;Terrabacteria group;Tenericutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;Mycoplasma hominis;Mycoplasma hominis ATCC 23114 NC_014760.1 cellular organisms;Bacteria;Terrabacteria group;Tenericutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;Mycoplasma bovis;Mycoplasma bovis PG45 real 0m3.200s user 0m5.392s sys 0m0.224sReplacing fasta header
$ seqkit replace -k seqs.fa.id2taxid2lineage -p '^(.+):.+' -r '{kv}' seqs.fa \ | seqkit replace -p ';' -r ',' >cellular organisms,Bacteria,Terrabacteria group,Tenericutes,Mollicutes,Mycoplasmatales,Mycoplasmataceae,Mycoplasma,Mycoplasma bovis,Mycoplasma bovis PG45 actg >cellular organisms,Bacteria,Terrabacteria group,Tenericutes,Mollicutes,Mycoplasmatales,Mycoplasmataceae,Mycoplasma,Mycoplasma hominis,Mycoplasma hominis ATCC 23114 ACTN
You want the lineage in format of "kingdom, phylum ... species" instead of full lineage? Fine:
$ time cat seqs.fa.id2taxid \
| taxonkit lineage -i 2 \
| taxonkit reformat -i 3
| sed 1d | cut -f 1,4 | tee seqs.fa.id2taxid2lineage2
NC_013511.1 Bacteria;Tenericutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;Mycoplasma hominis
NC_014760.1 Bacteria;Tenericutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;Mycoplasma bovis
real 0m5.183s
user 0m13.920s
sys 0m0.764s
$ seqkit replace -k seqs.fa.id2taxid2lineage2 -p '^(.+):.+' -r '{kv}' seqs.fa \
| seqkit replace -p ';' -r ','
>Bacteria,Tenericutes,Mollicutes,Mycoplasmatales,Mycoplasmataceae,Mycoplasma,Mycoplasma bovis
actg
>Bacteria,Tenericutes,Mollicutes,Mycoplasmatales,Mycoplasmataceae,Mycoplasma,Mycoplasma hominis
ACTN
It's exact what you want.
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Hello dllopezr,
could you please guide me where the full taxonomy is from and how it is connected to your current headers?
fin swimmer
The NCBI taxonomy always works in combination with the tax ID. I use the files merged.dmp and rankedlineage.dmp from here ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.zip and ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz.