diff utilities/validateFQ.py @ 0:6e75a84e9338 draft

planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utilities/validateFQ.py	Tue May 15 02:39:53 2018 -0400
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+#
+#	A quickie tool for validating the correctness of a FASTQ file
+#
+#	python validateFQ.py read1.fq [read2.fq]
+#
+
+import sys
+
+def get4lines(fn):
+	l1 = fn.readline().strip()
+	l2 = fn.readline().strip()
+	l3 = fn.readline().strip()
+	l4 = fn.readline().strip()
+	if any([l1,l2,l3,l4]) and not all([l1,l2,l3,l4]):
+		print '\nError: missing lines:\n'
+		print l1+'\n'+l2+'\n'+l3+'\n'+l4+'\n'
+		exit(1)
+	return (l1,l2,l3,l4)
+
+ALLOWED_QUAL = '!\"#$%&\'()*+,-./0123456789:;<=>?@ABCDEFGHIJ'
+ALLOWED_NUCL = 'ACGTN'
+
+def validate4lines(l1,l2,l3,l4):
+	failed = 0
+	# make sure lines contain correct delimiters
+	if l1[0] != '@' or l1[-2] != '/' or l3[0] != '+':
+		failed = 1
+	# make sure seq len == qual length
+	if len(l2) != len(l4):
+		failed = 2
+	# make sure seq string contains only valid characters
+	for n in l2:
+		if n not in ALLOWED_NUCL:
+			failed = 3
+	# make sure qual string contains only valid characters
+	for n in l4:
+		if n not in ALLOWED_QUAL:
+			failed = 4
+	if failed:
+		print '\nError: malformed lines:'
+		if failed == 1: print ' ---- invalid delimiters\n'
+		elif failed == 2: print ' ---- seq len != qual len\n'
+		elif failed == 3: print ' ---- seq contains invalid characters\n'
+		elif failed == 4: print ' ---- qual contains invalid characters\n'
+		print l1+'\n'+l2+'\n'+l3+'\n'+l4+'\n'
+		exit(1)
+
+f1 = open(sys.argv[1],'r')
+(l1_r1, l2_r1, l3_r1, l4_r1) = get4lines(f1)
+f2 = None
+if len(sys.argv) == 3:
+	f2 = open(sys.argv[2],'r')
+	(l1_r2, l2_r2, l3_r2, l4_r2) = get4lines(f2)
+
+while l1_r1:
+	# check line syntax
+	validate4lines(l1_r1,l2_r1,l3_r1,l4_r1)
+	if f2 != None:
+		validate4lines(l1_r2,l2_r2,l3_r2,l4_r2)
+		# make sure seq id is same for r1/r2
+		if l1_r1[:-1] != l1_r2[:-1]:
+			print '\nError: mismatched r1/r2 name:\n'
+			print l1_r1+'\n'+l1_r2+'\n'
+			exit(1)
+
+	# grab next 4 lines...
+	(l1_r1, l2_r1, l3_r1, l4_r1) = get4lines(f1)
+	if f2 != None:
+		(l1_r2, l2_r2, l3_r2, l4_r2) = get4lines(f2)
+
+if f2 != None:
+	f2.close()
+f1.close()
+
+print '\nPASSED WITH FLYING COLORS. GOOD DAY.\n'
+