Mercurial > repos > artbio > small_rna_maps
diff small_rna_maps.py @ 15:82fedc576024 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c1d96f7f028512aa4d8fcae3dd5f967cd445708e
| author | artbio |
|---|---|
| date | Sat, 06 Oct 2018 05:24:15 -0400 |
| parents | 3ea75c573429 |
| children | 600e2498bd21 |
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--- a/small_rna_maps.py Tue Apr 10 10:13:04 2018 -0400 +++ b/small_rna_maps.py Sat Oct 06 05:24:15 2018 -0400 @@ -54,15 +54,13 @@ map_dictionary[(chrom, 1, 'F')] = [] map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = [] for read in bam_object.fetch(chrom): - if (read.query_alignment_length >= minsize and - read.query_alignment_length <= maxsize): - positions = read.positions # a list of covered positions - if read.is_reverse: - map_dictionary[(chrom, positions[-1]+1, 'R')].append( - read.query_alignment_length) - else: - map_dictionary[(chrom, positions[0]+1, 'F')].append( - read.query_alignment_length) + positions = read.positions # a list of covered positions + if read.is_reverse: + map_dictionary[(chrom, positions[-1]+1, 'R')].append( + read.query_alignment_length) + else: + map_dictionary[(chrom, positions[0]+1, 'F')].append( + read.query_alignment_length) return map_dictionary def grouper(self, iterable, clust_distance):