diff options
Diffstat (limited to 'score_mers.py')
| -rwxr-xr-x | score_mers.py | 21 |
1 files changed, 12 insertions, 9 deletions
diff --git a/score_mers.py b/score_mers.py index 3409fc0..0a73cfb 100755 --- a/score_mers.py +++ b/score_mers.py @@ -10,11 +10,11 @@ import pdb fg_mers = {} bg_mers = {} -if(len(sys.argv) == 4): +if(len(sys.argv) == 5): selectivity_fn = sys.argv[1] - fg_fasta_fn = sys.argv[2] - bg_fasta_fn = sys.argv[3] - output_file = sys.argv[4] + fg_fasta_fn = sys.argv[2] + bg_fasta_fn = sys.argv[3] + output_file = sys.argv[4] else: print "please specify your inputs" print "ex: select_mers.py fg_counts_file fg_fasta_file bg_counts_file bg_fasta_file output_file" @@ -139,17 +139,19 @@ def pop_bg(mer): def main(): import time selected = [] - selectivty_fh = open(selectivity_fn, "r") + selectivity_fh = open(selectivity_fn, "r") # get our genome length fg_genome_length = os.path.getsize(fg_fasta_fn) bg_genome_length = os.path.getsize(bg_fasta_fn) - for row in selectivity_fn: + for row in selectivity_fh: (mer, fg_count, bg_count, selectivity) = row.split() fg_mers[mer] = Mer() + fg_mers[mer].pts = [] fg_mers[mer].count = fg_count bg_mers[mer] = Mer() + bg_mers[mer].pts = [] bg_mers[mer].count = bg_count selected.append([mer, selectivity]) @@ -160,6 +162,7 @@ def main(): # else: # selected = select_mers(fg_mers, bg_mers, max_select) selected = selected[-100:] + selected_mers = [row[0] for row in selected] pdb.set_trace() # print "searching through combinations of" # print selected @@ -167,10 +170,10 @@ def main(): print "Populating foreground locations" - map(pop_fg, selected) - map(pop_bg, selected) + map(pop_fg, selected_mers) + map(pop_bg, selected_mers) - scores = score_mers(selected) + scores = score_mers(selected_mers) print "fg_genome_length", fg_genome_length print "bg_genome_length", bg_genome_length |