read_input_file.py 文件源码

def _order_refalt_lexicographically(self, variants):
        # Also assert that chrom and pos are in order
        cp_groups = itertools.groupby(variants, key=lambda v:(v['chrom'], v['pos']))
        prev_chrom_index, prev_pos = -1, -1
        for cp, tied_variants in cp_groups:
            chrom_index = self._get_chrom_index(cp[0])
            if chrom_index < prev_chrom_index:
                raise PheWebError(
                    "The chromosomes in your file appear to be in the wrong order.\n" +
                    "The required order is: {!r}\n".format(chrom_order_list) +
                    "But in your file, the chromosome {!r} came after the chromosome {!r}\n".format(
                        cp[0], chrom_order_list[prev_chrom_index]))
            if chrom_index == prev_chrom_index and cp[1] < prev_pos:
                raise PheWebError(
                    "The positions in your file appear to be in the wrong order.\n" +
                    "In your file, the position {!r} came after the position {!r} on chromsome {!r}\n".format(
                        cp[1], prev_pos, cp[0]))
            prev_chrom_index, prev_pos = chrom_index, cp[1]
            for v in sorted(tied_variants, key=lambda v:(v['ref'], v['alt'])):
                yield v