Mercurial > repos > galaxyp > retrieve_ensembl_bed

annotate retrieve_ensembl_bed.py @ 1:c3d600729b6f draft

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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 e385fe93df68
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887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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1 #!/usr/bin/env python
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2 """
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3 #
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4 #------------------------------------------------------------------------------
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5 # University of Minnesota
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6 # Copyright 2017, Regents of the University of Minnesota
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7 #------------------------------------------------------------------------------
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8 # Author:
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9 #
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10 # James E Johnson
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11 #
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12 #------------------------------------------------------------------------------
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13 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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14
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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15 from __future__ import print_function
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16
0
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17 import argparse
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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18 import re
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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19 import sys
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21 from bedutil import bed_from_line
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23 from ensembl_rest import get_toplevel, get_transcripts_bed, max_region
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26 def __main__():
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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27 parser = argparse.ArgumentParser(
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28 description='Retrieve Ensembl cDNAs in BED format')
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29 parser.add_argument(
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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30 '-s', '--species', default='human',
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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31 help='Ensembl Species to retrieve')
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32 parser.add_argument(
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33 '-R', '--regions', action='append', default=[],
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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34 help='Restrict Ensembl retrieval to regions e.g.:'
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35 + ' X,2:20000-25000,3:100-500+')
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36 parser.add_argument(
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37 '-B', '--biotypes', action='append', default=[],
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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38 help='Restrict Ensembl biotypes to retrieve')
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39 parser.add_argument(
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40 '-X', '--extended_bed', action='store_true', default=False,
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41 help='Include the extended columns returned from Ensembl')
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42 parser.add_argument(
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43 '-U', '--ucsc_chrom_names', action='store_true', default=False,
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44 help='Use the UCSC names for Chromosomes')
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45 parser.add_argument(
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46 '-t', '--toplevel', action='store_true',
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47 help='Print Ensembl toplevel for species')
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48 parser.add_argument(
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49 'output',
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50 help='Output BED filepath, or for stdout: "-"')
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51 parser.add_argument('-v', '--verbose', action='store_true', help='Verbose')
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52 parser.add_argument('-d', '--debug', action='store_true', help='Debug')
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53 args = parser.parse_args()
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54 species = args.species
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55 out_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout
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56 biotypes = ';'.join(['biotype=%s' % bt.strip()
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57 for biotype in args.biotypes
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58 for bt in biotype.split(',') if bt.strip()])
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59
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60 selected_regions = dict() # chrom:(start, end)
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61 region_pat = '^([^:]+)(?::(\d*)(?:-(\d+)([+-])?)?)?'
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62 if args.regions:
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63 for entry in args.regions:
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64 if not entry:
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65 continue
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66 regs = [x.strip() for x in entry.split(',') if x.strip()]
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67 for reg in regs:
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68 m = re.match(region_pat, reg)
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69 if m:
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70 (chrom, start, end, strand) = m.groups()
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71 if chrom:
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72 if chrom not in selected_regions:
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73 selected_regions[chrom] = []
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74 selected_regions[chrom].append([start, end, strand])
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75 if args.debug:
1
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76 print("selected_regions: %s" % selected_regions, file=sys.stderr)
0
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77
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78 def retrieve_region(species, ref, start, stop, strand):
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79 transcript_count = 0
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
80 regions = list(range(start, stop, max_region))
0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
81 if not regions or regions[-1] < stop:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
82 regions.append(stop)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
83 for end in regions[1:]:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
84 bedlines = get_transcripts_bed(species, ref, start, end,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
85 strand=strand, params=biotypes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
86 if args.debug:
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
87 print("%s\t%s\tstart: %d\tend: %d\tcDNA transcripts:%d" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
88 (species, ref, start, end, len(bedlines)),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
89 file=sys.stderr)
0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
90 # start, end, seq
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
91 for i, bedline in enumerate(bedlines):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
92 if args.debug:
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
93 print("%s\n" % (bedline), file=sys.stderr)
0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
94 if not args.ucsc_chrom_names:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
95 bedline = re.sub('^[^\t]+', ref, bedline)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
96 try:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
97 if out_wtr:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
98 out_wtr.write(bedline.replace(',\t', '\t')
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
99 if args.extended_bed
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
100 else str(bed_from_line(bedline)))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
101 out_wtr.write("\n")
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
102 out_wtr.flush()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
103 except Exception as e:
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
104 print("BED error (%s) : %s\n" % (e, bedline),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
105 file=sys.stderr)
0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
106 start = end + 1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
107 return transcript_count
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
108
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
109 coord_systems = get_toplevel(species)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
110 if 'chromosome' in coord_systems:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
111 ref_lengths = dict()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
112 for ref in sorted(coord_systems['chromosome'].keys()):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
113 length = coord_systems['chromosome'][ref]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
114 ref_lengths[ref] = length
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
115 if args.toplevel:
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
116 print("%s\t%s\tlength: %d" % (species, ref, length),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
117 file=sys.stderr)
0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
118 if selected_regions:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
119 transcript_count = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
120 for ref in sorted(selected_regions.keys()):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
121 if ref in ref_lengths:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
122 for reg in selected_regions[ref]:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
123 (_start, _stop, _strand) = reg
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
124 start = int(_start) if _start else 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
125 stop = int(_stop) if _stop else ref_lengths[ref]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
126 strand = '' if not _strand else ':1'\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
127 if _strand == '+' else ':-1'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
128 transcript_count += retrieve_region(species, ref,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
129 start, stop,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
130 strand)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
131 if args.debug or args.verbose:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
132 length = stop - start
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
133 print("%s\t%s:%d-%d%s\tlength: %d\ttrancripts:%d" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
134 (species, ref, start, stop, strand,
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
135 length, transcript_count),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
136 file=sys.stderr)
0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
137 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
138 strand = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
139 start = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
140 for ref in sorted(ref_lengths.keys()):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
141 length = ref_lengths[ref]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
142 transcript_count = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
143 if args.debug:
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
144 print("Retrieving transcripts: %s\t%s\tlength: %d" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
145 (species, ref, length), file=sys.stderr)
0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
146 transcript_count += retrieve_region(species, ref, start,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
147 length, strand)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
148 if args.debug or args.verbose:
1
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
149 print("%s\t%s\tlength: %d\ttrancripts:%d" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
150 (species, ref, length, transcript_count),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents: 0
diff changeset
151 file=sys.stderr)
0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
152
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
153
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
154 if __name__ == "__main__":
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
155 __main__()