diff options
| -rw-r--r-- | Makefile | 4 | ||||
| -rwxr-xr-x | src/score_mers.py | 21 | ||||
| -rw-r--r-- | src/sequence_end_points.c (renamed from src/sequence_length.c) | 1 |
3 files changed, 24 insertions, 2 deletions
@@ -3,7 +3,7 @@ CC = gcc CFLAGS = -O3 -s -mtune=native -Wall -DVERSION=$(VERSION) -Wextra DEST = /usr/local/bin/ -all: output_dir bin/strstream bin/filter_melting_range bin/strstreamone +all: output_dir bin/strstream bin/filter_melting_range bin/strstreamone bin/sequence_end_points output_dir: mkdir -p bin @@ -11,6 +11,8 @@ bin/strstream: src/strstream.c $(CC) src/strstream.c -o bin/strstream $(CLIBS) $(CFLAGS) bin/strstreamone: src/strstreamone.c $(CC) src/strstreamone.c -o bin/strstreamone $(CLIBS) $(CFLAGS) +bin/sequence_end_points: src/sequence_end_points.c + $(CC) src/sequence_end_points.c -o bin/sequence_end_points $(CLIBS) $(CFLAGS) bin/filter_melting_range: src/filter_melting_range.c $(CC) src/filter_melting_range.c -o bin/filter_melting_range $(CLIBS) $(CFLAGS) diff --git a/src/score_mers.py b/src/score_mers.py index 6f0c6db..5c1a194 100755 --- a/src/score_mers.py +++ b/src/score_mers.py @@ -15,6 +15,8 @@ import pdb fg_mers = {} bg_mers = {} +seq_ends = [] + if(len(sys.argv) == 5): selectivity_fn = sys.argv[1] fg_fasta_fn = sys.argv[2] @@ -181,8 +183,13 @@ def score(combination): for mer in combination: fg_pts = fg_pts + fg_mers[mer].pts + fg_pts = fg_pts + seq_ends + fg_pts.sort() + if fg_pts[0] is not 0: + fg_pts = [0] + fg_pts + # fg distances fg_dist = np.diff(fg_pts) @@ -221,6 +228,18 @@ def score(combination): return [combination, score, fg_mean_dist, fg_std_dist, bg_ratio] +def load_end_points(fn): + + end_points = [] + + cmd = "sequence_end_points < " + fn + + points_fh = Popen(cmd, stdout=PIPE, shell=True) + for line in points_fh.stdout: + end_points.append(int(line)) + + return end_points + def load_heterodimer_dic(selected_mers): ''' Generate a heterodimer dict which contains every possible combination of @@ -265,6 +284,8 @@ def main(): selected_mers = [row[0] for row in selected] # print selected_mers + print "Populating sequence end points" + seq_ends = load_end_points(fg_fasta_fn) print "Populating foreground locations" map(pop_fg, selected_mers) diff --git a/src/sequence_length.c b/src/sequence_end_points.c index 3df7175..dc03dd9 100644 --- a/src/sequence_length.c +++ b/src/sequence_end_points.c @@ -24,7 +24,6 @@ int main() { for(i = 0; i < len; i++) { if(buffer[i] == '>') { printf("%llu\n", seq_length); - seq_length = 0; header = true; continue; } |