Python script recovers the genbank ids for all the nucleotide entries linked to a taxon id.

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.

taxid_2_gbids.py

Python

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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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