Mercurial > repos > jjohnson > bed_to_protein_map

annotate bed_to_protein_map.py @ 0:4702e7f629bb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
author jjohnson
date Mon, 20 Nov 2017 14:58:18 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
1 #!/usr/bin/env python
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
2 """
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
3 """
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
4 import sys
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
5 import os.path
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
6 import optparse
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
7
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
8 """
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
9 X 276352 291629 ENST00000430923 20 + 284187 291629 80,80,80 5 42,148,137,129,131 0,7814,12380,14295,15146
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
10 X 304749 318819 ENST00000326153 20 - 305073 318787 80,80,80 10 448,153,149,209,159,68,131,71,138,381 0,2610,2982,6669,8016,9400,10140,10479,12164,13689
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
11 grep ENST bed_to_protein_map.py | grep -v grep | ./bed_to_protein_map.py
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
12 """
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
13
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
14 def __main__():
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
15 #Parse Command Line
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
16 parser = optparse.OptionParser()
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
17 #I/O
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
18 parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' )
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
19 parser.add_option( '-c', '--column', type='int', dest='column', default=1, help='column ordinal with Ensembl transcript ID' )
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
20 parser.add_option( '-g', '--gtf', dest='gtf', default=None, help='GTF gene model file. Used to annotate NSJ peptide entries.')
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
21 parser.add_option( '-2', '--twobit', dest='twobit', default=None, help='Reference genome in UCSC twobit format')
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
22 parser.add_option( '-C', '--coding', dest='coding', action='store_true', default=False, help='Output coding BED line')
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
23 parser.add_option( '-o', '--output', dest='output', default=None, help='The output bed (else write to stdout)' )
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
24 parser.add_option( '-s', '--sqlitedb', dest='sqlitedb', default=None, help='The sqlitedb' )
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
25 parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Print debugging messages')
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
26 (options, args) = parser.parse_args()
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
27 ##INPUTS##
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
28 if options.input != None:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
29 try:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
30 inputPath = os.path.abspath(options.input)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
31 inputFile = open(inputPath, 'r')
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
32 except Exception, e:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
33 print >> sys.stderr, "failed: %s" % e
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
34 exit(2)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
35 else:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
36 inputFile = sys.stdin
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
37
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
38 if options.output != None:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
39 try:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
40 outputPath = os.path.abspath(options.output)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
41 outputFile = open(outputPath, 'w')
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
42 except Exception, e:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
43 print >> sys.stderr, "failed: %s" % e
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
44 exit(3)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
45 else:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
46 outputFile = sys.stdout
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
47
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
48 dbFile = None
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
49 if options.sqlitedb != None:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
50 try:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
51 dbPath = os.path.abspath(options.sqlitedb)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
52 dbFile = open(dbPath, 'w')
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
53 except Exception, e:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
54 print >> sys.stderr, "failed: %s" % e
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
55 exit(3)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
56
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
57
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
58 try:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
59 for linenum,line in enumerate(inputFile):
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
60 if options.debug:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
61 print >> sys.stderr, "%d: %s\n" % (linenum,line)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
62 if line.startswith('#'):
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
63 continue
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
64 if line.strip() == '':
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
65 continue
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
66 fields = line.rstrip('\r\n').split('\t')
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
67 if len(fields) < 12:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
68 print >> sys.stderr, "%d: %s\n" % (linenum,line)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
69 continue
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
70 (chrom,_chromStart,_chromEnd,name,score,strand,_thickStart,_thickEnd,itemRgb,_blockCount,blockSizes,blockStarts) = fields[0:12]
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
71 chromStart = int(_chromStart)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
72 chromEnd = int(_chromEnd)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
73 thickStart = int(_thickStart)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
74 thickEnd = int(_thickEnd)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
75 blockCount = int(_blockCount)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
76 blockSizes = [int(x) for x in blockSizes.split(',')]
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
77 blockStarts = [int(x) for x in blockStarts.split(',')]
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
78 if strand == '+':
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
79 cds_start = 0
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
80 cds_end = 0
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
81 for i in range(blockCount):
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
82 start = chromStart + blockStarts[i]
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
83 end = start + blockSizes[i]
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
84 if end < thickStart:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
85 continue
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
86 if start > thickEnd:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
87 break
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
88 if start < thickStart:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
89 start = thickStart
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
90 if end > thickEnd:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
91 end = thickEnd
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
92 cds_end = cds_start + (end - start)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
93 ##dbFile.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' % (name,chrom,start,end,strand,cds_start,cds_end))
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
94 outputFile.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' % (name,chrom,start,end,strand,cds_start,cds_end))
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
95 cds_start = cds_end
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
96 elif strand == '-':
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
97 cds_start = 0
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
98 cds_end = 0
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
99 for i in reversed(range(blockCount)):
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
100 start = chromStart + blockStarts[i]
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
101 end = start + blockSizes[i]
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
102 if end < thickStart:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
103 break
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
104 if start > thickEnd:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
105 continue
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
106 if start < thickStart:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
107 start = thickStart
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
108 if end > thickEnd:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
109 end = thickEnd
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
110 cds_end = cds_start + (end - start)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
111 outputFile.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' % (name,chrom,start,end,strand,cds_start,cds_end))
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
112 cds_start = cds_end
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
113 pass
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
114 except Exception, e:
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
115 print >> sys.stderr, "failed: %s" % e
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
116 exit(1)
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
117
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
118
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
119 if __name__ == "__main__" : __main__()
4702e7f629bb planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty
jjohnson
parents:
diff changeset
120