) parser.add_argument( "--species", nargs=1, required=True, help="species for which window coverage is to be determined, a .tsv file") parser.add_argument( "--output-prefix", nargs=1, required=True, help= "directory for outputs, windows are written to <output-prefix>/window_counts" ) args = parser.parse_args() outputs = paths.Outputs(args.output_prefix[0]) species = pd.read_csv(args.species[0], delimiter='\t') def coverage(windows_file, insertions_file, coverage_file): ''' generate coverage counts for each sliding window using bedtools coverage -counts ''' args = [ 'bedtools', 'coverage', "-counts", "-a", windows_file,
import pandas as pd import paths parser = argparse.ArgumentParser( description="Compare hotspot results") parser.add_argument("--species", nargs=1, required=True, help="species hotspots to be compared, a .tsv file") parser.add_argument("--output-a", nargs=1, required=True, help="directory for outputs-a") parser.add_argument("--output-b", nargs=1, required=True, help="directory for outputs-b") args = parser.parse_args() aout = paths.Outputs(args.output_a[0]) bout = paths.Outputs(args.output_b[0]) species = pd.read_csv(args.species[0], delimiter='\t') def read_results(outputs, species, genome): filename = outputs.significance_results_filename(species, genome) return pd.read_csv(filename, sep='\t') def compare_frames(a, b, columns, species, genome, precision): ra = read_results(a, species, genome) rb = read_results(b, species, genome) if precision == None: hsa = ra[columns] hsb = rb[columns] else: