if count % 10000 == 0:
print >>sys.stderr, "Record %s at %s" % (count, p[i]["end"])
-prog = re.compile(r'(.*?)(_12)?\.fastq(\.gz)?$')
+prog = re.compile(r'(.*?)(_[12])?\.fastq(\.gz)?$')
# Look for fastq files
for s in inp.all_streams():
for f in s.all_files():
name_pieces = prog.match(f.name())
- if name_pieces != None:
+ if name_pieces is not None:
if s.name() != ".":
# The downstream tool (run-command) only iterates over the top
# level of directories so if there are fastq files in
print >>sys.stderr, "fastq must be at the root of the collection"
sys.exit(1)
- if name_pieces.group(2) != None:
+ p = None
+ if name_pieces.group(2) is not None:
if name_pieces.group(2) == "_1":
p = [{}, {}]
p[0]["reader"] = s.files()[name_pieces.group(0)]
p = [{}]
p[0]["reader"] = s.files()[name_pieces.group(0)]
- if chunking:
- splitfastq(p)
- else:
- for i in xrange(0, len(p)):
- m = p[i]["reader"].as_manifest()[1:]
- manifest_list.append(["./_" + str(piece), m[:-1]])
- piece += 1
-
-manifest_text = "\n".join(" ".join(m) for m in manifest_list)
+ if p is not None:
+ if chunking:
+ splitfastq(p)
+ else:
+ for i in xrange(0, len(p)):
+ m = p[i]["reader"].as_manifest().split()
+ m[0] = "./_" + str(piece)
+ manifest_list.append(m)
+ piece += 1
+
+manifest_text = "\n".join(" ".join(m) for m in manifest_list) + "\n"
arvados.current_task().set_output(manifest_text)