How to pass a list of gene ids to url?

Question

I'm trying to pass a list of gene ids to url. gl stores a list of gene ids. I need "?term=" to iterate over the elements in the list and perform the function defined.

import re
import urllib2

def sr():
    gl = [6323,6513]

    # need to pass the list gl here:
    s = urllib2.urlopen('http://www.ncbi.nlm.nih.gov/gene/?term=','r')

    h = s.read()
    s.close()
    acc = re.search('gi=(.+?)&amp',h)
    if acc:
            ac = acc.group(1)
            f = open("E:/t.txt", "w")
            f.write(ac);
            f.close()

Answer 1

I'm not positive I understand what you're looking for, but perhaps urllib.urlencode is what you're looking for? urlencode will generate a query string. You can pass this, along with the base URL to urllib.urlopen .

I'm assuming the values for term are supposed to be comma-delimited?

gl = [6323,6513]
params = urllib.urlencode({"term": ','.join(map(str, gl))})
s urllib.urlopen('http://www.ncbi.nlm.nih.gov/gene/', params)

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As Peter Cock mentioned in the comments, you're better off using Entrez, NCBI's official API ( guide here ). Bio.Entrez provides a nice interface.