Mercurial > repos > jjohnson > iedb_api

comparison iedb_api.py @ 3:153d5fa7af53 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
author jjohnson
date Wed, 26 Feb 2020 16:27:06 -0500
parents 4a89ba6cfc63
children a14128950578
comparison
equal deleted inserted replaced
2:883cdf0ffae5 3:153d5fa7af53
3 import argparse 3 import argparse
4 import os.path 4 import os.path
5 import re 5 import re
6 import sys 6 import sys
7 import time 7 import time
8
9 from urllib.error import HTTPError 8 from urllib.error import HTTPError
10 from urllib.parse import urlencode, unquote 9 from urllib.parse import unquote, urlencode
11 from urllib.request import urlopen 10 from urllib.request import urlopen
12 11
13 mhci_methods = ['recommended', 'consensus', 12 mhci_methods = ['recommended', 'consensus',
14 'netmhcpan_ba', 'netmhcpan_el', 13 'netmhcpan_ba', 'netmhcpan_el',
15 'ann', 'smmpmbec', 'smm', 14 'ann', 'smmpmbec', 'smm',
184 msg = '%s %s\n%s' % (url, unquote(req_data), 183 msg = '%s %s\n%s' % (url, unquote(req_data),
185 ''.join(data)) 184 ''.join(data))
186 warn_err(msg, exit_code=1) 185 warn_err(msg, exit_code=1)
187 if line.find('eptide') > 0: 186 if line.find('eptide') > 0:
188 header = "#%s%s" %\ 187 header = "#%s%s" %\
189 ("ID\t" if seqid else "", line) 188 ("ID\t" if seqid else "", line)
190 if args.debug: 189 if args.debug:
191 print(header, file=sys.stderr) 190 print(header, file=sys.stderr)
192 continue 191 continue
193 elif method == 'Bepipred' and line.find('Residue') > 0: 192 elif method == 'Bepipred' and line.find('Residue') > 0:
194 header2 = "#%s%s" %\ 193 header2 = "#%s%s" %\
195 ("ID\t" if seqid else "", line) 194 ("ID\t" if seqid else "", line)
196 if args.debug: 195 if args.debug:
197 print(header2, file=sys.stderr) 196 print(header2, file=sys.stderr)
198 rslts = results2 197 rslts = results2
199 continue 198 continue
200 if seqid: 199 if seqid: