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July 17, 2017 19:37
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Transfrom content of Kallisto matrix, used for in silico ribotyping of C. difficile in this case
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#!/usr/bin/env python | |
"""Transform ribotype data. Input matrix | |
is a transposed output from bac_seq""" | |
from __future__ import print_function | |
from __future__ import division | |
import sys | |
import os | |
import optparse | |
def test_file(option, opt_str, value, parser): | |
try: | |
with open(value): setattr(parser.values, option.dest, value) | |
except IOError: | |
print('%s file cannot be opened' % option) | |
sys.exit() | |
def transpose_matrix(matrix): | |
out_matrix = open("transposed_matrix.matrix", "w") | |
reduced = [ ] | |
for line in open(matrix, "rU"): | |
newline=line.strip("\n") | |
fields = newline.split("\t") | |
reduced.append(fields) | |
test=map(list, zip(*reduced)) | |
for x in test: | |
out_matrix.write("\t".join(x)+"\n") | |
out_matrix.close() | |
def main(matrix, min_percent): | |
transpose_matrix(matrix) | |
print("Genome hits:") | |
for line in open("transposed_matrix.matrix", "rU"): | |
newline = line.strip() | |
fields = newline.split() | |
if fields[0] == "target": | |
pass | |
else: | |
values = [] | |
to_write = [] | |
for x in fields[1:]: | |
values.append(int(x)) | |
max_value = max(values) | |
for value in values: | |
try: | |
if float(value)/max_value > float(min_percent): | |
to_write.append("1") | |
else: | |
to_write.append("0") | |
except: | |
to_write.append("0") | |
if "0" in to_write[1:]: | |
pass | |
else: | |
print(fields[0]) | |
os.system("rm transposed_matrix.matrix") | |
if __name__ == "__main__": | |
usage="usage: %prog [options]" | |
parser = optparse.OptionParser(usage=usage) | |
parser.add_option("-m", "--matrix", dest="matrix", | |
help="/path/to/kallisto_merged_matrix [REQUIRED]", | |
type="string", action="callback", callback=test_file) | |
parser.add_option("-p", "--min_percent", dest="min_percent", | |
help="minimum percent of maximum to be called present, defaults to 0.2", | |
type="float", action="store", default="0.2") | |
options, args = parser.parse_args() | |
mandatories = ["matrix"] | |
for m in mandatories: | |
if not getattr(options, m, None): | |
print("\nMust provide %s.\n" %m) | |
parser.print_help() | |
exit(-1) | |
main(options.matrix,options.min_percent) |
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