Mercurial > repos > artbio > small_rna_maps
diff small_rna_maps.py @ 1:40972a8dfab9 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit ad60e6655aabe30246043d95f14646b2527c9255
| author | artbio |
|---|---|
| date | Mon, 24 Jul 2017 12:31:04 -0400 |
| parents | 6d48150495e3 |
| children | 507383cce5a8 |
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--- a/small_rna_maps.py Mon Jul 24 06:28:45 2017 -0400 +++ b/small_rna_maps.py Mon Jul 24 12:31:04 2017 -0400 @@ -51,8 +51,6 @@ for pos in positions: if not map_dictionary[(chrom, pos+1, 'F')]: map_dictionary[(chrom, pos+1, 'F')] = [] - if not map_dictionary[(chrom, pos+1, 'R')]: - map_dictionary[(chrom, pos+1, 'R')] = [] if read.is_reverse: map_dictionary[(chrom, positions[-1]+1, 'R')].append(read.query_alignment_length) @@ -113,7 +111,6 @@ for chrom in self.chromosomes: coverage_dictionary[(chrom, 1, 'F')] = 0 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0 - for key in map_dictionary: coverage = self.bam_object.count_coverage( reference=key[0], @@ -132,7 +129,7 @@ {chrom: {polarity: {size: nbre of reads}}} ''' size_dictionary = defaultdict(lambda: defaultdict( - lambda: defaultdict( int ))) + lambda: defaultdict(int))) # to track empty chromosomes for chrom in self.chromosomes: if self.bam_object.count(chrom) == 0: