Mercurial > repos > galaxyp > gffcompare_to_bed

comparison gffcompare_to_bed.py @ 2:9a4cfc910674 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
author galaxyp
date Tue, 07 Apr 2020 11:36:42 -0400
parents 7e572e148175
children ba5368c19dbd
comparison
equal deleted inserted replaced
1:0f62097d7c1a 2:9a4cfc910674
29 self.strand = '-' if str(strand).startswith('-') else '+' 29 self.strand = '-' if str(strand).startswith('-') else '+'
30 self.thickStart = int(thickStart) if thickStart else self.chromStart 30 self.thickStart = int(thickStart) if thickStart else self.chromStart
31 self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd 31 self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd
32 self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100' 32 self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100'
33 self.blockCount = int(blockCount) 33 self.blockCount = int(blockCount)
34 if isinstance(blockSizes, str) or isinstance(blockSizes, unicode): 34 if isinstance(blockSizes, str):
35 self.blockSizes = [int(x) for x in blockSizes.split(',')] 35 self.blockSizes = [int(x) for x in blockSizes.split(',')]
36 elif isinstance(blockSizes, list): 36 elif isinstance(blockSizes, list):
37 self.blockSizes = [int(x) for x in blockSizes] 37 self.blockSizes = [int(x) for x in blockSizes]
38 else: 38 else:
39 self.blockSizes = blockSizes 39 self.blockSizes = blockSizes
40 if isinstance(blockStarts, str) or isinstance(blockSizes, unicode): 40 if isinstance(blockStarts, str):
41 self.blockStarts = [int(x) for x in blockStarts.split(',')] 41 self.blockStarts = [int(x) for x in blockStarts.split(',')]
42 elif isinstance(blockStarts, list): 42 elif isinstance(blockStarts, list):
43 self.blockStarts = [int(x) for x in blockStarts] 43 self.blockStarts = [int(x) for x in blockStarts]
44 else: 44 else:
45 self.blockStarts = blockStarts 45 self.blockStarts = blockStarts
91 score, strand, frame, attributes) = fields 91 score, strand, frame, attributes) = fields
92 attribute = {i[0]: i[1].strip('"') for i in [j.strip().split(' ') 92 attribute = {i[0]: i[1].strip('"') for i in [j.strip().split(' ')
93 for j in attributes.rstrip(';').split(';')]} 93 for j in attributes.rstrip(';').split(';')]}
94 if feature == 'transcript': 94 if feature == 'transcript':
95 if args.debug: 95 if args.debug:
96 print >> sys.stderr, "%s\t%s"\ 96 sys.stderr.write("%s\t%s\n" % ('\t'.join([seqname, source,
97 % ('\t'.join([seqname, source, feature, 97 feature, start, end, score, strand, frame]),
98 start, end, score, strand, frame]), 98 attribute))
99 attribute)
100 if bed is not None: 99 if bed is not None:
101 write_bed_entry(bed) 100 write_bed_entry(bed)
102 bed = None 101 bed = None
103 class_code = attribute['class_code'].strip('"')\ 102 class_code = attribute['class_code'].strip('"')\
104 if 'class_code' in attribute else None 103 if 'class_code' in attribute else None