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This python script recovers the genbank ids for all the nucleotide entries linked to a taxon id. The number of requests is minimized using the retmax and retstart parameters provided by the Entrez Utilities.
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#!/usr/bin/env python | |
import xml.etree.ElementTree as ET | |
import sys, urllib, urllib2 | |
eutils_base_url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/" | |
def get_ids(taxid): | |
accession_numbers =[] | |
retstart = 0 | |
iteration_step = 10000 | |
while True: | |
result = esearch(db = "nucleotide", term = "txid%s[Organism:exp]"%taxid, retstart = retstart, retmax = iteration_step) | |
try: | |
result = ET.fromstring(result) | |
ids = [] | |
if result.find('IdList') is not None: | |
for id in result.find('IdList').findall('Id'): | |
ids.append(id.text) | |
result = esummary(db = "nucleotide", ids = ids, retmax = iteration_step) | |
result = ET.fromstring(result) | |
for docsum in result.findall('DocSum'): | |
for item in docsum.findall("Item[@Name='Caption']"): | |
accession_numbers.append(item.text) | |
else: | |
break | |
except Exception, e: | |
print e | |
retstart += iteration_step | |
return accession_numbers | |
def esearch(db, term, retstart = 0, retmax = 20): | |
response = urllib.urlopen("%sesearch.fcgi?db=%s&term=%s&retstart=%i&retmax=%i"%(eutils_base_url, db, term, retstart, retmax)) | |
content = str(response.read()) | |
response.close() | |
return content | |
def esummary(db, ids, retstart = 0, retmax = 20): | |
data = { | |
'db':db, | |
'id':','.join(ids) | |
} | |
data = urllib.urlencode(data) | |
req = urllib2.Request("%sesummary.fcgi"%eutils_base_url, data) | |
response = urllib2.urlopen(req) | |
content = str(response.read()) | |
response.close() | |
return content | |
if __name__ == '__main__': | |
taxid = None | |
if "-id" in sys.argv: | |
taxid = sys.argv[sys.argv.index("-id")+1] | |
if not taxid: | |
print "Usage: taxid_2_gbids.py -id taxid" | |
print "Example: taxid_2_gbids.py -id 4754" | |
sys.exit(-1) | |
ids = get_ids(taxid) | |
print ids | |
print "%i ids found..."%len(ids) |
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