comparison 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

0:6d48150495e3

            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 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)
                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],

        '''
        Takes a map_dictionary and returns a dictionary of sizes:
        {chrom: {polarity: {size: nbre of reads}}}
        '''
        size_dictionary = defaultdict(lambda: defaultdict(
                                      lambda: defaultdict( int )))
        #  to track empty chromosomes
        for chrom in self.chromosomes:
            if self.bam_object.count(chrom) == 0:
                size_dictionary[chrom]['F'][10] = 0
        for key in map_dictionary:

1:40972a8dfab9

            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],

        '''
        Takes a map_dictionary and returns a dictionary of sizes:
        {chrom: {polarity: {size: nbre of reads}}}
        '''
        size_dictionary = defaultdict(lambda: defaultdict(
                                      lambda: defaultdict(int)))
        #  to track empty chromosomes
        for chrom in self.chromosomes:
            if self.bam_object.count(chrom) == 0:
                size_dictionary[chrom]['F'][10] = 0
        for key in map_dictionary: