diff options
| -rwxr-xr-x | src/score_mers.py | 26 |
1 files changed, 17 insertions, 9 deletions
diff --git a/src/score_mers.py b/src/score_mers.py index ac7564d..8994815 100755 --- a/src/score_mers.py +++ b/src/score_mers.py @@ -4,10 +4,11 @@ import os from multiprocessing import Pool from multiprocessing import cpu_count -from subprocess import * + +from subprocess import Popen +from subprocess import PIPE + from itertools import combinations -from itertools import ifilter -from itertools import imap import numpy as np import pdb @@ -96,15 +97,18 @@ def populate_locations(selected_mers, mer_dic, input_fn): # strip file of header and delete newlines cmds.append("grep -v '^>' " + input_fn + " | tr -d '\\n' | strstream ") # reverse file, strip and delete newlines - cmds.append("tac " + input_fn + " | rev | grep -v '>$' | tr -d '\\n' | tr [ACGT] [TGCA] | strstream ") + cmds.append("tac " + input_fn + \ + "| rev " \ + "| grep -v '>$' " \ + "| tr -d '\\n' " \ + "| tr [ACGT] [TGCA] | strstream ") for cmd in cmds: - fid, merlist_fn = tempfile.mkstemp() + _, merlist_fn = tempfile.mkstemp() # write our mers out to a fifi merlist_fh = open(merlist_fn, 'w') for mer in selected_mers: - print mer merlist_fh.write(mer + '\n') merlist_fh.flush() @@ -121,6 +125,11 @@ def populate_locations(selected_mers, mer_dic, input_fn): def filter_mers(combination): + ''' + filter out mers that are either inside other mers, + or don't fit the heterodimer requirement. + ''' + for combo in combinations(combination, 2): if heterodimer_dic[combo]: return True @@ -204,7 +213,7 @@ def score(combination): # return without calculating scores if any objects are higher than our max distance if any(dist > max_mer_distance for dist in fg_dist): #return [combination, "max", max(fg_dist)] - return None + return None # bg counts bg_counts = 0 @@ -269,8 +278,6 @@ def main(): Score Combinations For All Sizes ''' - import time - selected = [] selectivity_fh = open(selectivity_fn, "r") # load our mer list into python @@ -286,6 +293,7 @@ def main(): bg_mers[mer] = [] print "Populating sequence end points" + global seq_ends seq_ends = load_end_points(fg_fasta_fn) print "Populating foreground locations" |