From acc1534c45a33b37368cf82dec3d6eb6fedb9442 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Wed, 22 Jan 2014 13:31:04 -0500 Subject: split --- select_mers.py | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) (limited to 'select_mers.py') diff --git a/select_mers.py b/select_mers.py index a4657d4..21306cc 100755 --- a/select_mers.py +++ b/select_mers.py @@ -33,13 +33,13 @@ def select_mers(fg_mers, bg_mers): # populate our bg_arr and fg_arr as well as our mer arr. for mer in fg_mers.keys(): mers.append(mer); - bg_arr.append(bg_mers[mer] + 1); + bg_arr.append(bg_mers.get(mer, 1)); fg_arr.append(fg_mers[mer]); fg_arr = np.array(fg_arr, dtype='f'); bg_arr = np.array(bg_arr, dtype='f'); - selectivity = (fg_arr/fg_genome_length) / (bg_arr/bg_genome_length) + selectivity = (fg_arr / bg_arr) arr = [(mers[i], fg_arr[i], bg_arr[i], selectivity[i]) for i in range(len(mers))] @@ -55,40 +55,29 @@ def select_mers(fg_mers, bg_mers): def main(): - fg_count_fh = open(fg_count_fn, "r") bg_count_fh = open(bg_count_fn, "r") # copy in our fg_mers and counts - print "populating our mers dictionary" for mers,fh in [(fg_mers, fg_count_fh), (bg_mers, bg_count_fh)]: for line in fh: (mer, count) = line.split() mers[mer] = int(count) if min_mer_count >= 1: - print "removing that are less frequent than: ", min_mer_count for mer in fg_mers.keys(): if(fg_mers[mer] < min_mer_count): del fg_mers[mer] if mer in bg_mers: del bg_mers[mer] - print "removing useless mers from the background" for mer in bg_mers.keys(): if mer not in fg_mers: del bg_mers[mer] - print "adding empty mers to the background" - for mer in fg_mers: - if mer not in bg_mers: - bg_mers[mer] = 0 - - print fg_genome_length - print bg_genome_length selected = select_mers(fg_mers, bg_mers) for row in selected: - print row[0] +"\t"+str(row[1]) + "\t" + str(row[2]) + str(row[3]) + print row[0] +"\t"+str("%d" % row[1]) + "\t" + str("%d" % row[2]) + "\t" + str("%.5f" % row[3]) if __name__ == "__main__": sys.exit(main()) -- cgit v1.2.3