comparison small_rna_map.py @ 6:f924a33e1eef draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 19a447cd21c746c852cf7434b5df423504baf383

5:d65045e976e6

    def compute_size(self, map_dictionary):
        '''
        Takes a map_dictionary and returns a dictionary of sizes:
        {chrom: {size: {polarity: nbre of reads}}}
        '''
        size_dictionary = defaultdict(lambda: defaultdict(lambda: defaultdict( int )))
        for key in map_dictionary:
            for size in map_dictionary[key]:
                try:
                    size_dictionary[key[0]][key[2]][size] += 1
                except KeyError:
                    size_dictionary[key[0]][key[2]][size] = 1
        return size_dictionary

    def write_size_table(self, out):
        '''
        Dataset, Chromosome, Polarity, Size, Nbr_reads

6:f924a33e1eef

    def compute_size(self, map_dictionary):
        '''
        Takes a map_dictionary and returns a dictionary of sizes:
        {chrom: {size: {polarity: nbre of reads}}}
        '''
        size_dictionary = defaultdict(lambda: defaultdict(
                                      lambda: defaultdict( int )))
        for key in map_dictionary:
            if len(map_dictionary) == 0:
                #  to track empty chromosomes
                size_dictionary[key[0]][key[2]][size] = 0
                continue
            for size in map_dictionary[key]:
                size_dictionary[key[0]][key[2]][size] += 1
        return size_dictionary

    def write_size_table(self, out):
        '''
        Dataset, Chromosome, Polarity, Size, Nbr_reads