)
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:
