Mercurial > repos > galaxyp > retrieve_ensembl_bed

annotate retrieve_ensembl_bed.py @ 2:e385fe93df68 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
author galaxyp
date Mon, 07 Oct 2019 16:14:19 -0400
parents c3d600729b6f
children
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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
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15 from __future__ import print_function
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16
0
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17 import argparse
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18 import re
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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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25
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26 def __main__():
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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(
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30 '-s', '--species', default='human',
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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=[],
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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 '-i', '--interval_file', default=None,
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
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38 help='Regions from a bed, gff, or interval file')
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
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39 parser.add_argument(
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40 '-f', '--interval_format', choices=['bed','gff','interval'], default='interval',
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
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41 help='Interval format has TAB-separated columns: Seq, Start, End, Strand')
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42 parser.add_argument(
0
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43 '-B', '--biotypes', action='append', default=[],
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44 help='Restrict Ensembl biotypes to retrieve')
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45 parser.add_argument(
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46 '-X', '--extended_bed', action='store_true', default=False,
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47 help='Include the extended columns returned from Ensembl')
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48 parser.add_argument(
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49 '-U', '--ucsc_chrom_names', action='store_true', default=False,
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50 help='Use the UCSC names for Chromosomes')
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51 parser.add_argument(
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52 '-t', '--toplevel', action='store_true',
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53 help='Print Ensembl toplevel for species')
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54 parser.add_argument(
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55 'output',
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56 help='Output BED filepath, or for stdout: "-"')
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57 parser.add_argument('-v', '--verbose', action='store_true', help='Verbose')
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58 parser.add_argument('-d', '--debug', action='store_true', help='Debug')
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59 args = parser.parse_args()
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60 species = args.species
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61 out_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout
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62 biotypes = ';'.join(['biotype=%s' % bt.strip()
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63 for biotype in args.biotypes
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64 for bt in biotype.split(',') if bt.strip()])
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65
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66 selected_regions = dict() # chrom:(start, end)
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67 region_pat = '^([^:]+)(?::(\d*)(?:-(\d+)([+-])?)?)?'
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68 if args.regions:
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69 for entry in args.regions:
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70 if not entry:
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71 continue
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72 regs = [x.strip() for x in entry.split(',') if x.strip()]
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73 for reg in regs:
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74 m = re.match(region_pat, reg)
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75 if m:
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76 (chrom, start, end, strand) = m.groups()
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77 if chrom:
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78 if chrom not in selected_regions:
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79 selected_regions[chrom] = []
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80 selected_regions[chrom].append([start, end, 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
81 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
82 print("selected_regions: %s" % selected_regions, 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
83
2
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
84 if args.interval_file:
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
85 pat = r'^(?:chr)?([^\t]+)(?:\t(\d+)(?:\t(\d+)(?:\t([+-])?)?)?)?.*'
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
86 if args.interval_format == 'bed':
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
87 pat = r'^(?:chr)?([^\t]+)\t(\d+)\t(\d+)(?:(?:\t[^\t]+\t[^\t]+\t)([+-]))?.*'
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
88 elif args.interval_format == 'gff':
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
89 pat = r'^(?:chr)?([^\t]+)\t(\d+)\t(\d+)(?:(?:\t[^\t]+\t[^\t]+\t)([+-]))?.*'
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
90 with open(args.interval_file,'r') as fh:
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
91 for i, line in enumerate(fh):
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
92 if line.startswith('#'):
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
93 continue
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
94 m = re.match(pat, line.rstrip())
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
95 if m:
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
96 (chrom, start, end, strand) = m.groups()
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
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97 if chrom:
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
98 if chrom not in selected_regions:
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
99 selected_regions[chrom] = []
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
diff changeset
100 selected_regions[chrom].append([start, end, strand])
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
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101 if args.debug:
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
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102 print("selected_regions: %s" % selected_regions, file=sys.stderr)
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
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103
e385fe93df68 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
galaxyp
parents: 1
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104
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
105 def retrieve_region(species, ref, start, stop, 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
106 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
107 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
108 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
109 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
110 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
111 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
112 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
113 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
114 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
115 (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
116 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
117 # 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:
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118 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:
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119 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
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120 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
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121 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:
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122 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
123 try:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
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124 if out_wtr:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
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diff changeset
125 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
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diff changeset
126 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
127 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
128 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
129 out_wtr.flush()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
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diff changeset
130 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
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131 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
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132 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:
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133 start = end + 1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
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134 return transcript_count
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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diff changeset
135
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
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diff changeset
136 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
137 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
138 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
139 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
140 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
141 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:
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142 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
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143 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
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diff changeset
144 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
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diff changeset
145 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
146 transcript_count = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
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diff changeset
147 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
148 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
149 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
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diff changeset
150 (_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
151 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
152 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
153 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
154 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
155 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
156 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
157 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
158 if args.debug or args.verbose:
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galaxyp
parents:
diff changeset
159 length = stop - start
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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160 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
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161 (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
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162 length, transcript_count),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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163 file=sys.stderr)
0
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164 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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165 strand = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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166 start = 0
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167 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
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168 length = ref_lengths[ref]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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169 transcript_count = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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170 if args.debug:
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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171 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
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172 (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
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173 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
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174 length, strand)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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175 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
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176 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
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177 (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
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178 file=sys.stderr)
0
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179
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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180
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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181 if __name__ == "__main__":
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182 __main__()