comparison small_rna_maps.py @ 3:ed8b0142538d draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1

2:507383cce5a8

                else:
                    map_dictionary[(chrom, positions[0]+1,
                                    'F')].append(read.query_alignment_length)
        return map_dictionary

    def compute_map(self, map_dictionary, out):
        '''
        takes a map_dictionary as input and writes
        a readmap_dictionary {(chromosome,read_position,polarity):
                              number_of_reads}
        in an open file handler out

            header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
                      "Polarity", method]
        F.write('\t'.join(header) + '\n')
        for input, sample in zip(inputs, samples):
            mapobj = Map(input, sample)
            token = {"Counts": mapobj.compute_map,
                     "Max": mapobj.compute_max,
                     "Mean": mapobj.compute_mean,
                     "Median": mapobj.compute_median,
                     "Coverage": mapobj.compute_coverage,
                     "Size": mapobj.compute_size}

3:ed8b0142538d

                else:
                    map_dictionary[(chrom, positions[0]+1,
                                    'F')].append(read.query_alignment_length)
        return map_dictionary

    def compute_readcount(self, map_dictionary, out):
        '''
        takes a map_dictionary as input and writes
        a readmap_dictionary {(chromosome,read_position,polarity):
                              number_of_reads}
        in an open file handler out

            header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
                      "Polarity", method]
        F.write('\t'.join(header) + '\n')
        for input, sample in zip(inputs, samples):
            mapobj = Map(input, sample)
            token = {"Counts": mapobj.compute_readcount,
                     "Max": mapobj.compute_max,
                     "Mean": mapobj.compute_mean,
                     "Median": mapobj.compute_median,
                     "Coverage": mapobj.compute_coverage,
                     "Size": mapobj.compute_size}