From f363df2ac34c34b1c2f223bb5a81c456a764ac38 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Fri, 21 Mar 2014 13:42:54 -0400
Subject: add end of sequences in as points in our array

---
 src/score_mers.py         | 21 ++++++++++++++++++
 src/sequence_end_points.c | 54 ++++++++++++++++++++++++++++++++++++++++++++++
 src/sequence_length.c     | 55 -----------------------------------------------
 3 files changed, 75 insertions(+), 55 deletions(-)
 create mode 100644 src/sequence_end_points.c
 delete mode 100644 src/sequence_length.c

(limited to 'src')

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_end_points.c b/src/sequence_end_points.c
new file mode 100644
index 0000000..dc03dd9
--- /dev/null
+++ b/src/sequence_end_points.c
@@ -0,0 +1,54 @@
+// Copyright 2013 Calvin Morrison
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+#include <stdbool.h>
+#include <errno.h>
+int main() {
+
+	size_t len = 0;
+
+	char buffer[4096];
+	bool header = false;
+
+	len = fread(&buffer, 1, 1, stdin);
+
+	unsigned long long seq_length = 0;
+	if(!errno) {
+		if(buffer[0] == '>') {
+			header = true;
+
+			while((len = fread(&buffer, 1, 4096, stdin)) != 0) {
+				size_t i = 0;                                                                    
+				for(i = 0; i < len; i++) {
+					if(buffer[i] == '>') {
+						printf("%llu\n", seq_length);
+						header = true;
+						continue;
+					}   
+					else if(buffer[i] == '\n' && header == true) {
+						header = false;
+						continue;
+					}
+					if(header == false && buffer[i] != '\n') { 
+						seq_length++;
+					}   
+				}   
+			}   
+		} 
+		else { 
+			fprintf(stderr, "this does not look like a fasta file\n"); 
+			return EXIT_FAILURE;
+		}
+	} 
+	else { 
+		fprintf(stderr, "could not read file\n"); 
+		return EXIT_FAILURE;
+	}
+
+	printf("%llu\n", seq_length);
+
+	return EXIT_SUCCESS;
+}
+
diff --git a/src/sequence_length.c b/src/sequence_length.c
deleted file mode 100644
index 3df7175..0000000
--- a/src/sequence_length.c
+++ /dev/null
@@ -1,55 +0,0 @@
-// Copyright 2013 Calvin Morrison
-#include <stdio.h>
-#include <stdlib.h>
-#include <unistd.h>
-#include <stdint.h>
-#include <stdbool.h>
-#include <errno.h>
-int main() {
-
-	size_t len = 0;
-
-	char buffer[4096];
-	bool header = false;
-
-	len = fread(&buffer, 1, 1, stdin);
-
-	unsigned long long seq_length = 0;
-	if(!errno) {
-		if(buffer[0] == '>') {
-			header = true;
-
-			while((len = fread(&buffer, 1, 4096, stdin)) != 0) {
-				size_t i = 0;                                                                    
-				for(i = 0; i < len; i++) {
-					if(buffer[i] == '>') {
-						printf("%llu\n", seq_length);
-						seq_length = 0;
-						header = true;
-						continue;
-					}   
-					else if(buffer[i] == '\n' && header == true) {
-						header = false;
-						continue;
-					}
-					if(header == false && buffer[i] != '\n') { 
-						seq_length++;
-					}   
-				}   
-			}   
-		} 
-		else { 
-			fprintf(stderr, "this does not look like a fasta file\n"); 
-			return EXIT_FAILURE;
-		}
-	} 
-	else { 
-		fprintf(stderr, "could not read file\n"); 
-		return EXIT_FAILURE;
-	}
-
-	printf("%llu\n", seq_length);
-
-	return EXIT_SUCCESS;
-}
-
-- 
cgit v1.2.3