e06b04eacb0eefdd392e54a0ec2a4f24c22ef50c,cnvlib/target.py,,assign_names,#Any#Any#Any#,59

Before Change

    Replace the interval gene names with those at the same loc in refFlat.txt
    
    ref_genes = read_refflat_genes(refflat_fname)
    region_rows = sorted(region_rows,
                         key=lambda row: (row[0], row[3], row[1], row[2]))
    for (chrom, strand), chr_rows in groupby(region_rows,
                                             lambda row: (row[0], row[3])):
        if (chrom, strand) not in ref_genes:
            ngfrills.echo("Chromosome", chrom, "strand", strand,
                          "not in annotations")
            continue
        genes_in_chrom = iter(ref_genes[(chrom, strand)])
        ex_start, ex_end, ex_name = next(genes_in_chrom)
        for row in chr_rows:
            start, end = row[1:3]

After Change

                if (chrom, std) in ref_genes:
                    strands_with_genes.extend(ref_genes[(chrom, std)])
            if strands_with_genes:
                genes_in_chrom = iter(sorted(strands_with_genes))
            else:
                ngfrills.echo("Chromosome", chrom, strand, "not in annotations")
                continue
        else:

Instances