comparison 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

3:ed8b0142538d

            map_dictionary[(chrom, 1, 'F')] = []
            map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
        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)
                else:
                    map_dictionary[(chrom, positions[0]+1,

        '''
        coverage_dictionary = dict()
        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],
                                                start=key[1]-1,
                                                end=key[1],

4:a6b9a081064b

            map_dictionary[(chrom, 1, 'F')] = []
            map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
        for chrom in self.chromosomes:
            for read in bam_object.fetch(chrom):
                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,

        '''
        coverage_dictionary = dict()
        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],
                                                start=key[1]-1,
                                                end=key[1],