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NabaviLab / SEACON

A tool for allele-specific copy number profiling.
GNU General Public License v3.0
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Bug in core.py #4

Open xikanfeng2 opened 3 weeks ago

xikanfeng2 commented 3 weeks ago 
"seacon/core.py", line 156, in prep_baf
    reader.write_region_file(args['out_dir'], 'filtered_regions.bed', shared_bins, stats=filtered_stats)
NameError: name 'filtered_stats' is not defined

variable filtered_stats is not defined in this function.

xikanfeng2 commented 3 weeks ago 
    if len(shared_bins) < len(bin_coords):
            chrom_names = reader.get_chrom_names(args['chrom_names'])
            chrom_lens = reader.get_chrom_lens(args['reference'], chrom_names)
            regions = reader.get_bins_from_chromlens(chrom_lens, args['bin_size'])
            full_region_path = reader.write_region_file(args['out_dir'], 'full_regions.bed', regions)
            gc = reader.get_gc(args['reference'], full_region_path, args['bedtools'])
            mapp = reader.get_mapp(args['out_dir'], full_region_path, args['bigwig'], args['map_file'])
            filtered_regions, filtered_stats = reader.filter_bins_gc_mapp(regions, gc, mapp)
            reader.write_region_file(args['out_dir'], 'filtered_regions.bed', shared_bins, stats=filtered_stats)
            reader.write_cell_names(os.path.join(args['out_dir'], 'cells.txt'), shared_cells)
            print(readcounts_df.shape)
            cell_avgs = readcounts_df.mean(axis=1)
            RDR_df = readcounts_df.div(cell_avgs, axis=0)
            RDR_df = RDR_df.round(5)
            readcounts_df.to_csv(os.path.join(args['out_dir'], 'readcounts.tsv'), sep='\t')
            RDR_df.to_csv(os.path.join(args['out_dir'], 'RDR.tsv'), sep='\t')

I refactored the code as shown above. One important point to note is that the readcounts_df also needs to be resaved; otherwise, the seacon call step will throw a dimension mismatch error.