Getting genes id from taxonomy

Question

[theLegend]

Hello,

Is there an easy way to get all gene ids from a species using Biopython ?

Thanks for your help

[Sej Modha]

You can use BioPython module Bio.Entrez for this. Alternatively, you can also use NCBI Entrez Direct UNIX E-utilities for the same.

Answer 1

[Andrzej Zielezinski]

BioPython code:

from Bio import Entrez

Entrez.email = "[e-mail]" 
handle = Entrez.esearch(
    db="gene", 
    term="Homo sapiens[Organism]",
    retmax=100000)
record = Entrez.read(handle)

with open('results.txt', 'w') as oh:
    for id in record["IdList"]:
        oh.write(id + '\n')

Output (first 5 lines of results.txt):

7157
1956
7124
348
7422

You can also use BioMart RESTful access. You just need a XML file with search parameters:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >

    <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
        <Attribute name = "ensembl_gene_id" />
        <Attribute name = "entrezgene" />
        <Attribute name = "hgnc_symbol" />
    </Dataset>
</Query>

Convert it into a single line and put it after the "query=" below. Run the following command in shell:

wget -O results.txt 'http://www.ensembl.org/biomart/martservice?query=<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6"><Dataset name="hsapiens_gene_ensembl" interface="default"><Attribute name="ensembl_gene_id"/><Attribute name="entrezgene"/><Attribute name="hgnc_symbol"/></Dataset></Query>'

Output (first 5 lines of results.txt):

ENSG00000210049     MT-TF
ENSG00000211459 4549    MT-RNR1
ENSG00000210077     MT-TV
ENSG00000210082 4550    MT-RNR2
ENSG00000209082     MT-TL1