diff baseline/script_imgt.py @ 83:729738462297 draft

"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"

--- a/baseline/script_imgt.py	Thu Feb 25 10:32:32 2021 +0000
+++ b/baseline/script_imgt.py	Wed Sep 15 12:24:06 2021 +0000
@@ -1,86 +1,86 @@
-#import xlrd #avoid dep
-import argparse
-import re
-
-parser = argparse.ArgumentParser()
-parser.add_argument("--input", help="Excel input file containing one or more sheets where column G has the gene annotation, H has the sequence id and J has the sequence")
-parser.add_argument("--ref", help="Reference file")
-parser.add_argument("--output", help="Output file")
-parser.add_argument("--id", help="ID to be used at the '>>>' line in the output")
-
-args = parser.parse_args()
-
-print "script_imgt.py"
-print "input:", args.input
-print "ref:", args.ref
-print "output:", args.output
-print "id:", args.id
-
-refdic = dict()
-with open(args.ref, 'rU') as ref:
-	currentSeq = ""
-	currentId = ""
-	for line in ref:
-		if line.startswith(">"):
-			if currentSeq is not "" and currentId is not "":
-				refdic[currentId[1:]] = currentSeq
-			currentId = line.rstrip()
-			currentSeq = ""
-		else:
-			currentSeq += line.rstrip()
-	refdic[currentId[1:]] = currentSeq
-
-print "Have", str(len(refdic)), "reference sequences"
-
-vPattern = [r"(IGHV[0-9]-[0-9ab]+-?[0-9]?D?\*\d{1,2})"]#,
-#						r"(TRBV[0-9]{1,2}-?[0-9]?-?[123]?)",
-#						r"(IGKV[0-3]D?-[0-9]{1,2})",
-#						r"(IGLV[0-9]-[0-9]{1,2})",
-#						r"(TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?)",
-#						r"(TRGV[234589])",
-#						r"(TRDV[1-3])"]
-
-#vPattern = re.compile(r"|".join(vPattern))
-vPattern = re.compile("|".join(vPattern))
-
-def filterGene(s, pattern):
-    if type(s) is not str:
-        return None
-    res = pattern.search(s)
-    if res:
-        return res.group(0)
-    return None
-
-
-
-currentSeq = ""
-currentId = ""
-first=True
-with open(args.input, 'r') as i:
-	with open(args.output, 'a') as o:
-		o.write(">>>" + args.id + "\n")
-		outputdic = dict()
-		for line in i:
-			if first:
-				first = False
-				continue
-			linesplt = line.split("\t")
-			ref = filterGene(linesplt[1], vPattern)
-			if not ref or not linesplt[2].rstrip():
-				continue
-			if ref in outputdic:
-				outputdic[ref] += [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]
-			else:
-				outputdic[ref] = [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]
-		#print outputdic
-		
-		for k in outputdic.keys():
-			if k in refdic:
-				o.write(">>" + k + "\n")
-				o.write(refdic[k] + "\n")
-				for seq in outputdic[k]:
-					#print seq
-					o.write(">" + seq[0] + "\n")
-					o.write(seq[1] + "\n")
-			else:
-				print k + " not in reference, skipping " + k
+#import xlrd #avoid dep
+import argparse
+import re
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--input", help="Excel input file containing one or more sheets where column G has the gene annotation, H has the sequence id and J has the sequence")
+parser.add_argument("--ref", help="Reference file")
+parser.add_argument("--output", help="Output file")
+parser.add_argument("--id", help="ID to be used at the '>>>' line in the output")
+
+args = parser.parse_args()
+
+print("script_imgt.py")
+print("input:", args.input)
+print("ref:", args.ref)
+print("output:", args.output)
+print("id:", args.id)
+
+refdic = dict()
+with open(args.ref, 'rU') as ref:
+	currentSeq = ""
+	currentId = ""
+	for line in ref:
+		if line.startswith(">"):
+			if currentSeq is not "" and currentId is not "":
+				refdic[currentId[1:]] = currentSeq
+			currentId = line.rstrip()
+			currentSeq = ""
+		else:
+			currentSeq += line.rstrip()
+	refdic[currentId[1:]] = currentSeq
+
+print("Have", str(len(refdic)), "reference sequences")
+
+vPattern = [r"(IGHV[0-9]-[0-9ab]+-?[0-9]?D?\*\d{1,2})"]#,
+#						r"(TRBV[0-9]{1,2}-?[0-9]?-?[123]?)",
+#						r"(IGKV[0-3]D?-[0-9]{1,2})",
+#						r"(IGLV[0-9]-[0-9]{1,2})",
+#						r"(TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?)",
+#						r"(TRGV[234589])",
+#						r"(TRDV[1-3])"]
+
+#vPattern = re.compile(r"|".join(vPattern))
+vPattern = re.compile("|".join(vPattern))
+
+def filterGene(s, pattern):
+    if type(s) is not str:
+        return None
+    res = pattern.search(s)
+    if res:
+        return res.group(0)
+    return None
+
+
+
+currentSeq = ""
+currentId = ""
+first=True
+with open(args.input, 'r') as i:
+	with open(args.output, 'a') as o:
+		o.write(">>>" + args.id + "\n")
+		outputdic = dict()
+		for line in i:
+			if first:
+				first = False
+				continue
+			linesplt = line.split("\t")
+			ref = filterGene(linesplt[1], vPattern)
+			if not ref or not linesplt[2].rstrip():
+				continue
+			if ref in outputdic:
+				outputdic[ref] += [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]
+			else:
+				outputdic[ref] = [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]
+		#print outputdic
+		
+		for k in list(outputdic.keys()):
+			if k in refdic:
+				o.write(">>" + k + "\n")
+				o.write(refdic[k] + "\n")
+				for seq in outputdic[k]:
+					#print seq
+					o.write(">" + seq[0] + "\n")
+					o.write(seq[1] + "\n")
+			else:
+				print(k + " not in reference, skipping " + k)