Mercurial > repos > drosofff > fetch_fasta_from_ncbi

comparison retrieve_fasta_from_NCBI.py @ 12:0bec3cba5c56 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author drosofff
date Wed, 09 Nov 2016 11:27:31 -0500
parents 2c5375809c03
children 639daa4c3c1a
comparison
equal deleted inserted replaced
11:962054e7c2de 12:0bec3cba5c56
30 import time 30 import time
31 import urllib 31 import urllib
32 import urllib2 32 import urllib2
33 import httplib 33 import httplib
34 import re 34 import re
35
36
35 class Eutils: 37 class Eutils:
36 38
37 def __init__(self, options, logger): 39 def __init__(self, options, logger):
38 self.logger = logger 40 self.logger = logger
39 self.base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/" 41 self.base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
40 self.query_string = options.query_string 42 self.query_string = options.query_string
41 self.dbname = options.dbname 43 self.dbname = options.dbname
42 if options.outname: 44 if options.outname:
43 self.outname = options.outname 45 self.outname = options.outname
44 else: 46 else: