Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.py @ 30:183bf49fe77c draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d280e9be7cf96f4938a73ccf5985533109f3328f"
author artbio
date Sat, 05 Oct 2019 18:25:19 -0400
parents 8b5695592784
children f82badb66c34
comparison
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29:8b5695592784 30:183bf49fe77c
240 positions = read.positions # a list of covered positions 240 positions = read.positions # a list of covered positions
241 for pos in positions: 241 for pos in positions:
242 if not map_dictionary[(chrom, pos+1, 'F')]: 242 if not map_dictionary[(chrom, pos+1, 'F')]:
243 map_dictionary[(chrom, pos+1, 'F')] = [] 243 map_dictionary[(chrom, pos+1, 'F')] = []
244 for key in map_dictionary: 244 for key in map_dictionary:
245 if 'R' in key:
246 continue
245 coverage = self.bam_object.count_coverage( 247 coverage = self.bam_object.count_coverage(
246 contig=key[0], 248 contig=key[0],
247 start=key[1]-1, 249 start=key[1]-1,
248 stop=key[1], 250 stop=key[1],
249 quality_threshold=quality) 251 quality_threshold=quality)