diff baseline/script_imgt.py @ 81:b6f9a640e098 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/baseline/script_imgt.py	Fri Feb 19 15:10:54 2021 +0000
@@ -0,0 +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