INNER CODE UNIT · Python

validate_input

nloyfer/wgbs_tools · src/python/add_cpg_counts.py:112

    def validate_input(self):
        # validate output dir:
        if not (op.isdir(self.out_dir)):
            raise IllegalArgumentError(f'Invalid output dir: {self.out_dir}')

    def start_threads(self):
        """ Parse each chromosome file in a different process,
            and concatenate outputs to pat and unq files """
        print(datetime.datetime.now().isoformat() + ': *** starting processing of each chromosome')
        name = op.join(self.out_dir, pretty_name(self.bam_path))
        is_PE = is_pair_end(self.bam_path, self.gr.genome)
        if self.gr.region_str is None:
            final_path = name + f'.{self.args.suffix}' + BAM_SUFF
            params = []
            for c in set_regions(self.bam_path, self.gr):
                out_path_name = name + '_' + c
                params.append((self.bam_path, out_path_name, c, self.gr.genome,
                        is_PE, self.args.exclude_flags, self.args.mapq,

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