Mercurial > repos > artbio > small_rna_maps
diff small_rna_maps.py @ 4:a6b9a081064b draft
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 |
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--- a/small_rna_maps.py Tue Aug 22 12:05:47 2017 -0400 +++ b/small_rna_maps.py Fri Aug 25 12:22:03 2017 -0400 @@ -44,9 +44,6 @@ for chrom in self.chromosomes: for read in bam_object.fetch(chrom): positions = read.positions # a list of covered positions - for pos in positions: - if not map_dictionary[(chrom, pos+1, 'F')]: - map_dictionary[(chrom, pos+1, 'F')] = [] if read.is_reverse: map_dictionary[(chrom, positions[-1]+1, 'R')].append(read.query_alignment_length) @@ -120,6 +117,11 @@ for chrom in self.chromosomes: coverage_dictionary[(chrom, 1, 'F')] = 0 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0 + for read in self.bam_object.fetch(chrom): + positions = read.positions # a list of covered positions + for pos in positions: + if not map_dictionary[(chrom, pos+1, 'F')]: + map_dictionary[(chrom, pos+1, 'F')] = [] for key in map_dictionary: coverage = self.bam_object.count_coverage( reference=key[0],