INNER CODE UNIT · Python

validate_bed

nloyfer/wgbs_tools · src/python/add_cpg_counts.py:88

    def validate_bed(self):
        if self.bed_path is None:
            return
        df = load_bed(self.bed_path).iloc[:, :3]

        # check start before end
        if ((df['start'] >= df['end']).any()):
            eprint(f'[wt add_cpg_counts] bed file is not legal - end before start')
            raise IllegalArgumentError('Bed file is not legal')

        # check start is monotonic
        ref_chroms =  self.gr.genome.get_chroms()
        for chrom in ref_chroms:
            if not df[df['chr'] == chrom]['start'].is_monotonic_increasing:
                eprint(f'[wt add_cpg_counts] bed file is not sorted')
                raise IllegalArgumentError('Bed file is not sorted')

        # create tmp files from bed file (extend each region with +-1000 bp)

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