Mercurial > repos > iuc > ngsutils_bam_filter

comparison ngsutils/bed/__init__.py @ 2:7a68005de299 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
author iuc
date Sun, 27 Nov 2016 15:01:21 -0500
parents 4e4e4093d65d
children
comparison
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1:8187a729d9f4 2:7a68005de299
1 import os 1 import os
2
2 import ngsutils.support.ngs_utils 3 import ngsutils.support.ngs_utils
3 import pysam 4 import pysam
4 5
5 6
6 class BedStreamer(object): 7 class BedStreamer(object):
29 cols.append('') 30 cols.append('')
30 31
31 return BedRegion(*cols) 32 return BedRegion(*cols)
32 except: 33 except:
33 raise StopIteration 34 raise StopIteration
34
35 35
36 36
37 class BedFile(object): 37 class BedFile(object):
38 ''' 38 '''
39 BED files are read in their entirety memory, in a series of bins. Each bin 39 BED files are read in their entirety memory, in a series of bins. Each bin
133 if (chrom, bin) in self._bins: 133 if (chrom, bin) in self._bins:
134 for region in self._bins[(chrom, bin)]: 134 for region in self._bins[(chrom, bin)]:
135 if strand and strand != region.strand: 135 if strand and strand != region.strand:
136 continue 136 continue
137 if start <= region.start <= end or start <= region.end <= end: 137 if start <= region.start <= end or start <= region.end <= end:
138 if not region in buf: 138 if region not in buf:
139 yield region 139 yield region
140 buf.add(region) 140 buf.add(region)
141 elif region.start < start and region.end > end: 141 elif region.start < start and region.end > end:
142 if not region in buf: 142 if region not in buf:
143 yield region 143 yield region
144 buf.add(region) 144 buf.add(region)
145 145
146 def tell(self): 146 def tell(self):
147 return self._tellpos 147 return self._tellpos