exposed fasta/q reader to mappy

python/minimap2.py

@@ -3,47 +3,14 @@
 import sys, getopt
 import mappy as mp
 
-def readfq(fp): # multi-line fasta/fastq parser
-	last = None
-	while True:
-		if not last:
-			for l in fp:
-				if l[0] in '>@':
-					last = l[:-1]
-					break
-		if not last: break
-		name, seqs, last = last[1:].split()[0], [], None
-		for l in fp:
-			if l[0] in '@+>':
-				last = l[:-1]
-				break
-			seqs.append(l[:-1])
-		if not last or last[0] != '+':
-			yield name, ''.join(seqs), None
-			if not last: break
-		else:
-			seq, leng, seqs = ''.join(seqs), 0, []
-			for l in fp:
-				seqs.append(l[:-1])
-				leng += len(l) - 1
-				if leng >= len(seq):
-					last = None
-					yield name, seq, ''.join(seqs);
-					break
-			if last:
-				yield name, seq, None
-				break
-
 def main(argv):
 	opts, args = getopt.getopt(argv[1:], "")
 	if len(args) < 2:
 		print("Usage: minimap2.py <ref.fa>|<ref.mmi> <query.fq>")
 		sys.exit(1)
 	a = mp.Aligner(args[0]) # load/build index
-	if not a:
-		print("ERROR: failed to load/build index")
-		return
-	for name, seq, qual in readfq(open(args[1])): # read one sequence
+	if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
+	for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
 		for h in a.map(seq): # traverse hits
 			print('{}\t{}\t{}'.format(name, len(seq), h))