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#!/usr/bin/python
"""
Create a matrix of many pairwise intersections; see \
:mod:`pybedtools.contrib.IntersectionMatrix` for more flexibility
"""
import collections
import time
import sys
import os.path as op
import argparse
import pybedtools
from pybedtools import BedTool, example_filename
usage = (
"""
Send in a list of `N` bed files, and this script will create an N by
N matrix of their intersections, or optionally, co-localization scores.
Run the example with::
%s --test > matrix.txt
You can then plot a quick heatmap in R with::
> m = as.matrix(read.table("matrix.txt"))
> heatmap(m)
"""
% sys.argv[0]
)
def get_name(fname):
return op.splitext(op.basename(fname))[0]
def actual_intersection(a, b):
return len(a.intersect(b, u=True))
def frac_of_a(a, b):
len_a = float(len(a))
return len(a.intersect(b, u=True)) / len_a
def enrichment_score(a, b, genome_fn, iterations=None, processes=None):
results = a.randomstats(
b, new=True, genome_fn=genome_fn, iterations=iterations, processes=processes
)
return (results["actual"] + 1) / (results["median randomized"] + 1)
def create_matrix(beds, func, verbose=False, **kwargs):
nfiles = len(beds)
total = nfiles ** 2
i = 0
matrix = collections.defaultdict(dict)
for fa in beds:
a = BedTool(fa)
for fb in beds:
i += 1
b = BedTool(fb)
if verbose:
sys.stderr.write("%(i)s of %(total)s: %(fa)s + %(fb)s\n" % locals())
sys.stderr.flush()
matrix[get_name(fa)][get_name(fb)] = func(a, b, **kwargs)
return matrix
def main():
"""
Creates a pairwise matrix containing overlapping feature counts for many
BED files
"""
ap = argparse.ArgumentParser(usage=usage)
ap.add_argument(
"beds",
nargs="*",
help="BED/GTF/GFF/VCF filenames, e.g., "
"in a directory of bed files, you can use *.bed",
)
ap.add_argument(
"--frac",
action="store_true",
help="Instead of counts, report fraction overlapped",
)
ap.add_argument(
"--enrichment",
action="store_true",
help="Run randomizations (default 1000, specify otherwise "
"with --iterations) on each pairwise comparison and "
"compute the enrichment score as "
"(actual intersection count + 1) / (median randomized + 1)",
)
ap.add_argument(
"--genome",
help="Required argument if --enrichment is "
'used. Needs to be a string assembly name like "dm3" or '
'"hg19"',
)
ap.add_argument(
"--iterations",
default=1000,
type=int,
help="Number of randomizations to perform for enrichement " "scores",
)
ap.add_argument(
"--processes",
default=None,
type=int,
help="Number of CPUs to use for randomization",
)
ap.add_argument(
"--test",
action="store_true",
help="Ignore any input BED " "files and use test BED files",
)
ap.add_argument(
"-v",
"--verbose",
action="store_true",
help="Be verbose: print which files are "
"currently being intersected and timing info at the end.",
)
args = ap.parse_args()
if not args.beds and not args.test:
ap.print_help()
sys.exit(1)
if args.test:
# insulator binding sites from ChIP-chip -- 4 proteins, 2 cell types
# Genes Dev. 2009 23(11):1338-1350
args.beds = [
example_filename(i)
for i in [
"Cp190_Kc_Bushey_2009.bed",
"Cp190_Mbn2_Bushey_2009.bed",
"CTCF_Kc_Bushey_2009.bed",
"CTCF_Mbn2_Bushey_2009.bed",
"SuHw_Kc_Bushey_2009.bed",
"SuHw_Mbn2_Bushey_2009.bed",
"BEAF_Mbn2_Bushey_2009.bed",
"BEAF_Kc_Bushey_2009.bed",
]
]
if args.enrichment:
FUNC = enrichment_score
genome_fn = pybedtools.chromsizes_to_file(pybedtools.chromsizes(args.genome))
kwargs = dict(
genome_fn=genome_fn, iterations=args.iterations, processes=args.processes
)
elif args.frac:
FUNC = frac_of_a
kwargs = {}
else:
FUNC = actual_intersection
kwargs = {}
t0 = time.time()
matrix = create_matrix(beds=args.beds, func=FUNC, verbose=args.verbose, **kwargs)
t1 = time.time()
nfiles = len(args.beds)
if args.verbose:
sys.stderr.write(
"Time to construct %s x %s matrix: %.1fs" % (nfiles, nfiles, (t1 - t0))
+ "\n"
)
keys = sorted(matrix.keys())
sys.stdout.write("\t" + "\t".join(keys) + "\n")
for k in keys:
sys.stdout.write(k)
for j in keys:
sys.stdout.write("\t" + str(matrix[k][j]))
sys.stdout.write("\n")
if __name__ == "__main__":
main()
|
