comparison small_rna_maps.py @ 31:f82badb66c34 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"

30:183bf49fe77c

        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:
            if 'R' in key:

31:f82badb66c34

        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 = sorted(read.positions)  # list of covered positions
                #  add flanking position at 0 to join
                #  the base line when plotting graph
                flanking = []
                for i in range(len(positions)-1):
                    right = positions[i+1]
                    left = positions[i]
                    if positions[i+1] - positions[i] > 2:
                        flanking.insert(0, right-1)
                        flanking.insert(0, left+1)
                    elif positions[i+1] - positions[i] == 2:
                        flanking.insert(0, left+1)
                positions = sorted(positions + flanking)
                if positions[0] > 0:
                    positions.insert(0, positions[0]-1)
                if positions[-1] < self.chromosomes[chrom] - 1:
                    positions.append(positions[-1]+1)
                for pos in positions:
                    if not map_dictionary[(chrom, pos+1, 'F')]:
                        map_dictionary[(chrom, pos+1, 'F')] = []
        for key in map_dictionary:
            if 'R' in key: