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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)