Mercurial > repos > galaxyp > retrieve_ensembl_bed
diff ensembl_rest.py @ 1:c3d600729b6f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
author | galaxyp |
---|---|
date | Mon, 22 Jan 2018 13:13:26 -0500 |
parents | 887e111c0919 |
children |
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--- a/ensembl_rest.py Sun Jan 14 14:11:53 2018 -0500 +++ b/ensembl_rest.py Mon Jan 22 13:13:26 2018 -0500 @@ -12,6 +12,8 @@ #------------------------------------------------------------------------------ """ +from __future__ import print_function +from __future__ import unicode_literals import sys @@ -28,10 +30,10 @@ def ensembl_rest(ext, headers): if debug: - print >> sys.stderr, "%s" % ext + print("%s" % ext, file=sys.stderr) r = requests.get(server+ext, headers=headers) if r.status_code == 429: - print >> sys.stderr, "response headers: %s\n" % r.headers + print("response headers: %s\n" % r.headers, file=sys.stderr) if 'Retry-After' in r.headers: sleep(r.headers['Retry-After']) r = requests.get(server+ext, headers=headers) @@ -47,12 +49,11 @@ r = ensembl_rest(ext, req_header) for species in r.json()['species']: results[species['name']] = species - print >> sys.stdout,\ - "%s\t%s\t%s\t%s\t%s"\ - % (species['name'], species['common_name'], + print("%s\t%s\t%s\t%s\t%s" % + (species['name'], species['common_name'], species['display_name'], species['strain'], - species['taxon_id']) + species['taxon_id']), file=sys.stdout) return results @@ -86,7 +87,7 @@ bed = [] param = params if params else '' req_header = {"Content-Type": "text/x-bed"} - regions = range(start, length, max_region) + regions = list(range(start, length, max_region)) if not regions or regions[-1] < length: regions.append(length) for end in regions[1:]: