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

#!/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)