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#!/usr/bin/env python2.7
import sys
import os
import argparse
mers = {}
debug = os.environ.get("debug", False)
from subprocess import Popen
from subprocess import PIPE
def get_sequence(pt):
for it, seq in enumerate(seq_ends, start=1):
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 = []
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 size_iterator(mer_arr):
for mer_len in set([ len(it) for it in mer_arr]):
mers = filter(lambda x: len(x) == mer_len, mer_arr)
yield mers
def populate_locations(mers, mer_dic, input_fn, length):
'''
Run the kmer_locations command, and parse in the integers that are output
by the command, and add it to mers[mer]
We also do the reverse compliment, so we subtract the length of the genome for it
'''
import tempfile
# write our mers out to a fifi
for n_mers in size_iterator(mers):
_, merlist_fn = tempfile.mkstemp()
merlist_fh = open(merlist_fn, 'w')
for mer in n_mers:
print mer
merlist_fh.write(mer + '\n')
merlist_fh.flush()
# add our merlist fn to our command
cmd = "kmer_locations -k " + str(len(n_mers[0])) + " -c -m \"" + merlist_fn + "\" -l -i \"" + input_fn + "\""
if(debug):
print "Executing", cmd
cmd_pipe = Popen(cmd, stdout=PIPE, shell=True)
for line in cmd_pipe.stdout:
line_s = line[:-1].split(" ")
if len(line_s) == 2:
mer_dic[line_s[0]].append([int(line_s[1]), 3])
elif len(line_s) == 3:
mer_dic[line_s[0]].append([length - int(line_s[1]), 5])
if cmd_pipe.wait() is not 0:
print "Executing", cmd, "failed"
exit()
merlist_fh.close()
def main():
parser = argparse.ArgumentParser(description="take a top-scores file, and \
create a set of files that contain the positions (and other information) in \
the foreground fasta file of each mer in that combination. ")
parser.add_argument("-f", "--fasta", help="input fasta file", required=True)
parser.add_argument("-s", "--scores", help="input scores file", required=True)
parser.add_argument("-o", "--output_directory", help="directory to output sets to.", required=True)
parser.add_argument("-n", "--number", help="output the first n sets", 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)
length = get_length(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, length)
pts = []
for mer in combination:
for pt in mers[mer]:
pts.append([pt[0], pt[1], mer, get_sequence(pt[0])])
pts = sorted(pts, key = lambda row: row[0])
fh.write("pt\tstrand\tmer\tsequence\n")
for pt in pts:
fh.write('\t'.join(str(x) for x in pt) + '\n')
nb_done += 1
if nb_done == args.number:
exit()
if __name__ == "__main__":
sys.exit(main())
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