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#!/usr/bin/env python
import sys
import os
import argparse
mers = {}
debug = False
from subprocess import Popen
from subprocess import PIPE
def get_sequence(pt):
for it, seq in enumerate(seq_ends):
if pt <= seq:
return it
def load_end_points(fn):
''' get all the points of the end of each sequence in a sample '''
end_points = [0]
cmd = "sequence_end_points < " + fn
if debug:
print "loading sequence end points"
print "executing: " + cmd
points_fh = Popen(cmd, stdout=PIPE, shell=True)
for line in points_fh.stdout:
end_points.append(int(line))
if points_fh.wait() is not 0:
print "executing", cmd, "failed"
return end_points
def get_length(fn):
''' get length of a genome ( number of base pairs )'''
cmd = 'grep "^>" ' + fn + " -v | tr -d '\\n' | wc -c"
if debug:
print "loading sequence end points"
print "executing: " + cmd
grep = Popen(cmd, stdout=PIPE, shell=True)
length = grep.stdout.readline()
length = int(length)
if grep.wait() is not 0:
print "executing", cmd, "failed"
return length
def populate_locations(selected_mers, mer_dic, input_fn, length):
'''
Run the strstreamone command, and parse in the integers that are output
by the command, and add it to mers[mer]
strstreamone just prints the location of a string argv[1] in stdout.
We also do the reverse compliment, using tac and tr piped together.
'''
import tempfile
cmds = []
# strip file of header and delete newlines
cmds.append(["grep -v '^>' " + input_fn + " | tr -d '\\n' | strstream ", False])
# reverse file, strip and delete newlines
cmds.append(["tac " + input_fn + \
"| rev " \
"| grep -v '>$' " \
"| tr -d '\\n' " \
"| tr [ACGT] [TGCA] | strstream ", True])
for (cmd, reverse) in cmds:
_, merlist_fn = tempfile.mkstemp()
# write our mers out to a fifi
merlist_fh = open(merlist_fn, 'w')
for mer in selected_mers:
merlist_fh.write(mer + '\n')
merlist_fh.flush()
# add our merlist fn to our command
cmd = cmd + " " + merlist_fn
strstream = Popen(cmd, stdout=PIPE, shell=True)
if reverse:
for line in strstream.stdout:
(mer, pos) = line.split(" ")
pos = length - int(pos)
mer_dic[selected_mers[int(mer)]].append(pos)
else:
for line in strstream.stdout:
(mer, pos) = line.split(" ")
mer_dic[selected_mers[int(mer)]].append(int(pos))
if strstream.wait() is not 0:
print "executing", cmd, "failed"
merlist_fh.close()
def main():
parser = argparse.ArgumentParser(description="score mers")
parser.add_argument("-f", "--fasta", help="input fasta file", required=True)
parser.add_argument("-s", "--scores", help="scores file", required=True)
parser.add_argument("-o", "--output_directory", help="scores file", required=True)
parser.add_argument("-n", "--number", help="output top n", required=False, type=int, default=20)
args = parser.parse_args()
if os.path.isfile(args.output_directory):
parser.error(args.output_directory + "must point to a directory")
elif not os.path.isdir(args.output_directory):
os.mkdir(args.output_directory)
score_fh = open(args.scores, "r")
global seq_ends
seq_ends = load_end_points(args.fasta)
nb_done = 0;
for line in score_fh:
# skip headers
if line.startswith("#"):
continue
# get mers
combination = line.split('\t')[1].split()
# open output
fh = open(args.output_directory + "/" + '-'.join(combination), 'w')
# populate only un-populated mers
new_populate = []
for mer in combination:
if mer not in mers:
mers[mer] = []
new_populate.append(mer)
if len(new_populate) is not 0:
populate_locations(new_populate, mers, args.fasta, get_length(args.fasta))
pts = []
for mer in combination:
for pt in mers[mer]:
pts.append([pt, mer, get_sequence(pt)])
pts = sorted(pts, key = lambda row: row[0])
for pt in pts:
fh.write(str(pt))
fh.write("\n")
nb_done += 1
if nb_done == args.number:
exit()
if __name__ == "__main__":
sys.exit(main())
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