# HG changeset patch
# User davidvanzessen
# Date 1427959883 14400
# Node ID c9f9623f1f7614edd3bb186bda68af0ff5b13099
# Parent  850857bc8605a3039eb8b18c62681f7f7f6e24c6
Uploaded

diff -r 850857bc8605 -r c9f9623f1f76 gene_identification.py
--- a/gene_identification.py	Wed Apr 01 05:26:52 2015 -0400
+++ b/gene_identification.py	Thu Apr 02 03:31:23 2015 -0400
@@ -170,7 +170,6 @@
 				pass
 			ID = linesplt[1]
 			currentIDHits = hits[ID]
-			print currentIDHits
 			possibleca = float(len(compiledregex["ca"]))
 			possiblecg = float(len(compiledregex["cg"]))
 			possiblecm = float(len(compiledregex["cm"]))
diff -r 850857bc8605 -r c9f9623f1f76 mutation_analysis.py
--- a/mutation_analysis.py	Wed Apr 01 05:26:52 2015 -0400
+++ b/mutation_analysis.py	Thu Apr 02 03:31:23 2015 -0400
@@ -72,6 +72,7 @@
 aggctatIndex = 0
 atagcctIndex = 0
 first = True
+IDlist = []
 with open(infile, 'r') as i:
 	for line in i:
 		if first:
@@ -93,6 +94,7 @@
 		WRCYCount[ID] = sum([1 for (x,y,z) in WRCY if z and z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
 		WACount[ID] = sum([1 for (x,y,z) in WA if z and z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
 		TWCount[ID] = sum([1 for (x,y,z) in TW if z and z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
+		IDlist += [ID]
 
 
 directory = outfile[:outfile.rfind("/") + 1]
@@ -124,3 +126,20 @@
 		y = valuedic["total"]
 		z = str(round(x / float(valuedic["total"]) * 100, 1))
 		o.write("," + str(x) + "," + str(y) + "," + z + "\n")
+
+
+#for testing
+seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt"
+first = True
+with open(seq_motif_file, 'w') as o:
+	for ID in IDlist:
+		if first:
+			o.write("ID\tRGYWC\tWRCY\tWA\tTW\n")
+			first = False
+			continue
+		print ID
+		print RGYWCount[ID]
+		print WRCYCount[ID]
+		print WACount[ID]
+		print TWCount[ID]
+		o.write(ID + "\t" + str(RGYWCount[ID]) + "\t" + str(WRCYCount[ID]) + "\t" + str(WACount[ID]) + "\t" + str(TWCount[ID]) + "\n")
diff -r 850857bc8605 -r c9f9623f1f76 wrapper.sh
--- a/wrapper.sh	Wed Apr 01 05:26:52 2015 -0400
+++ b/wrapper.sh	Thu Apr 02 03:31:23 2015 -0400
@@ -70,7 +70,7 @@
 		echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
 done < $outdir/result.txt
 echo "</table>" >> $output
-echo "<a href='unmatched.txt'>unmatched</a><br />" >> $output
+echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output
 
 
 echo "<img src='all.png'/><br />" >> $output