Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.py @ 4:a6b9a081064b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b58cb36616bf351278e57ec1949e9ebf3c3cdff1
author artbio
date Fri, 25 Aug 2017 12:22:03 -0400
parents ed8b0142538d
children 12c14642e6ac
comparison
equal deleted inserted replaced
3:ed8b0142538d 4:a6b9a081064b
42 map_dictionary[(chrom, 1, 'F')] = [] 42 map_dictionary[(chrom, 1, 'F')] = []
43 map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = [] 43 map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
44 for chrom in self.chromosomes: 44 for chrom in self.chromosomes:
45 for read in bam_object.fetch(chrom): 45 for read in bam_object.fetch(chrom):
46 positions = read.positions # a list of covered positions 46 positions = read.positions # a list of covered positions
47 for pos in positions:
48 if not map_dictionary[(chrom, pos+1, 'F')]:
49 map_dictionary[(chrom, pos+1, 'F')] = []
50 if read.is_reverse: 47 if read.is_reverse:
51 map_dictionary[(chrom, positions[-1]+1, 48 map_dictionary[(chrom, positions[-1]+1,
52 'R')].append(read.query_alignment_length) 49 'R')].append(read.query_alignment_length)
53 else: 50 else:
54 map_dictionary[(chrom, positions[0]+1, 51 map_dictionary[(chrom, positions[0]+1,
118 ''' 115 '''
119 coverage_dictionary = dict() 116 coverage_dictionary = dict()
120 for chrom in self.chromosomes: 117 for chrom in self.chromosomes:
121 coverage_dictionary[(chrom, 1, 'F')] = 0 118 coverage_dictionary[(chrom, 1, 'F')] = 0
122 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0 119 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0
120 for read in self.bam_object.fetch(chrom):
121 positions = read.positions # a list of covered positions
122 for pos in positions:
123 if not map_dictionary[(chrom, pos+1, 'F')]:
124 map_dictionary[(chrom, pos+1, 'F')] = []
123 for key in map_dictionary: 125 for key in map_dictionary:
124 coverage = self.bam_object.count_coverage( 126 coverage = self.bam_object.count_coverage(
125 reference=key[0], 127 reference=key[0],
126 start=key[1]-1, 128 start=key[1]-1,
127 end=key[1], 129 end=key[1],