Mercurial > repos > galaxyp > retrieve_ensembl_bed

annotate retrieve_ensembl_bed.py @ 0:da1b538b87e5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 13:13:47 -0500
parents
children 9c4a48f5d4e7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
1 #!/usr/bin/env python
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
2 """
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
3 #
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
4 #------------------------------------------------------------------------------
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
5 # University of Minnesota
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
6 # Copyright 2017, Regents of the University of Minnesota
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
7 #------------------------------------------------------------------------------
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
8 # Author:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
9 #
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
10 # James E Johnson
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
11 #
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
12 #------------------------------------------------------------------------------
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
13 """
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
14
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
15 from __future__ import print_function
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
16
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
17 import argparse
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
18 import re
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
19 import sys
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
20
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
21 from bedutil import bed_from_line
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
22
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
23 from ensembl_rest import get_toplevel, get_transcripts_bed, max_region
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
24
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
25
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
26 def __main__():
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
27 parser = argparse.ArgumentParser(
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
28 description='Retrieve Ensembl cDNAs in BED format')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
29 parser.add_argument(
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
30 '-s', '--species', default='human',
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
31 help='Ensembl Species to retrieve')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
32 parser.add_argument(
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
33 '-R', '--regions', action='append', default=[],
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
34 help='Restrict Ensembl retrieval to regions e.g.:'
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
35 + ' X,2:20000-25000,3:100-500+')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
36 parser.add_argument(
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
37 '-B', '--biotypes', action='append', default=[],
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
38 help='Restrict Ensembl biotypes to retrieve')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
39 parser.add_argument(
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
40 '-X', '--extended_bed', action='store_true', default=False,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
41 help='Include the extended columns returned from Ensembl')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
42 parser.add_argument(
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
43 '-U', '--ucsc_chrom_names', action='store_true', default=False,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
44 help='Use the UCSC names for Chromosomes')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
45 parser.add_argument(
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
46 '-t', '--toplevel', action='store_true',
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
47 help='Print Ensembl toplevel for species')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
48 parser.add_argument(
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
49 'output',
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
50 help='Output BED filepath, or for stdout: "-"')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
51 parser.add_argument('-v', '--verbose', action='store_true', help='Verbose')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
52 parser.add_argument('-d', '--debug', action='store_true', help='Debug')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
53 args = parser.parse_args()
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
54 species = args.species
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
55 out_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
56 biotypes = ';'.join(['biotype=%s' % bt.strip()
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
57 for biotype in args.biotypes
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
58 for bt in biotype.split(',') if bt.strip()])
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
59
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
60 selected_regions = dict() # chrom:(start, end)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
61 region_pat = '^([^:]+)(?::(\d*)(?:-(\d+)([+-])?)?)?'
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
62 if args.regions:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
63 for entry in args.regions:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
64 if not entry:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
65 continue
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
66 regs = [x.strip() for x in entry.split(',') if x.strip()]
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
67 for reg in regs:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
68 m = re.match(region_pat, reg)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
69 if m:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
70 (chrom, start, end, strand) = m.groups()
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
71 if chrom:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
72 if chrom not in selected_regions:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
73 selected_regions[chrom] = []
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
74 selected_regions[chrom].append([start, end, strand])
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
75 if args.debug:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
76 print("selected_regions: %s" % selected_regions, file=sys.stderr)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
77
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
78 def retrieve_region(species, ref, start, stop, strand):
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
79 transcript_count = 0
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
80 regions = list(range(start, stop, max_region))
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
81 if not regions or regions[-1] < stop:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
82 regions.append(stop)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
83 for end in regions[1:]:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
84 bedlines = get_transcripts_bed(species, ref, start, end,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
85 strand=strand, params=biotypes)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
86 if args.debug:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
87 print("%s\t%s\tstart: %d\tend: %d\tcDNA transcripts:%d" %
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
88 (species, ref, start, end, len(bedlines)),
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
89 file=sys.stderr)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
90 # start, end, seq
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
91 for i, bedline in enumerate(bedlines):
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
92 if args.debug:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
93 print("%s\n" % (bedline), file=sys.stderr)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
94 if not args.ucsc_chrom_names:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
95 bedline = re.sub('^[^\t]+', ref, bedline)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
96 try:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
97 if out_wtr:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
98 out_wtr.write(bedline.replace(',\t', '\t')
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
99 if args.extended_bed
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
100 else str(bed_from_line(bedline)))
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
101 out_wtr.write("\n")
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
102 out_wtr.flush()
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
103 except Exception as e:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
104 print("BED error (%s) : %s\n" % (e, bedline),
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
105 file=sys.stderr)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
106 start = end + 1
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
107 return transcript_count
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
108
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
109 coord_systems = get_toplevel(species)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
110 if 'chromosome' in coord_systems:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
111 ref_lengths = dict()
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
112 for ref in sorted(coord_systems['chromosome'].keys()):
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
113 length = coord_systems['chromosome'][ref]
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
114 ref_lengths[ref] = length
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
115 if args.toplevel:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
116 print("%s\t%s\tlength: %d" % (species, ref, length),
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
117 file=sys.stderr)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
118 if selected_regions:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
119 transcript_count = 0
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
120 for ref in sorted(selected_regions.keys()):
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
121 if ref in ref_lengths:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
122 for reg in selected_regions[ref]:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
123 (_start, _stop, _strand) = reg
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
124 start = int(_start) if _start else 0
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
125 stop = int(_stop) if _stop else ref_lengths[ref]
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
126 strand = '' if not _strand else ':1'\
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
127 if _strand == '+' else ':-1'
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
128 transcript_count += retrieve_region(species, ref,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
129 start, stop,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
130 strand)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
131 if args.debug or args.verbose:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
132 length = stop - start
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
133 print("%s\t%s:%d-%d%s\tlength: %d\ttrancripts:%d" %
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
134 (species, ref, start, stop, strand,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
135 length, transcript_count),
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
136 file=sys.stderr)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
137 else:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
138 strand = ''
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
139 start = 0
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
140 for ref in sorted(ref_lengths.keys()):
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
141 length = ref_lengths[ref]
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
142 transcript_count = 0
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
143 if args.debug:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
144 print("Retrieving transcripts: %s\t%s\tlength: %d" %
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
145 (species, ref, length), file=sys.stderr)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
146 transcript_count += retrieve_region(species, ref, start,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
147 length, strand)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
148 if args.debug or args.verbose:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
149 print("%s\t%s\tlength: %d\ttrancripts:%d" %
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
150 (species, ref, length, transcript_count),
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
151 file=sys.stderr)
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
152
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
153
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
154 if __name__ == "__main__":
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
155 __main__()