Question

TaxID to taxonomy (Entrez Direct: E-utilities on the Unix Command Line)

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2.5 years ago

Abu Bakar ▴ 10

Entrez Direct: E-utilities on the Unix Command Line

I would like to execute the following command but with a list where i have thousands tax ids (id). How to execute that?

efetch -db taxonomy -id 9606,7227,10090 -format xml | xtract -pattern Taxon \ -element TaxId ScientificName GenbankCommonName Division

Entrez • 1.1k views

ADD COMMENT • link updated 2.5 years ago by GenoMax 146k • written 2.5 years ago by Abu Bakar ▴ 10

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you either download the complete taxonomy table locally and query that one (with eg grep ) or you put the the efetch command in a for loop and loop over all your taxIDs.

ADD REPLY • link 2.5 years ago by lieven.sterck 15k

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thanks, how to do that, any suggestion? is at like that?

for i in tax_ids.txt;    do  efetch -db taxonomy -id $i -format xml | xtract -pattern Taxon \ -element TaxId ScientificName GenbankCommonName Division

ADD REPLY • link updated 2.5 years ago by GenoMax 146k • written 2.5 years ago by Abu Bakar ▴ 10

score 1 · Answer 1 · 2022-05-12

One way

$ more ids
9606
7227
10090

$ for i in `cat ids`; do  efetch -db taxonomy -id ${i} -format xml | xtract -pattern Taxon -element TaxId,ScientificName,GenbankCommonName,Division;done 
9606    Homo sapiens    human   Primates
7227    Drosophila melanogaster fruit fly   Invertebrates
10090   Mus musculus    house mouse Rodents