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Merge branch 'master' into 4951-request-vm
[arvados.git]
/
crunch_scripts
/
split-fastq.py
diff --git
a/crunch_scripts/split-fastq.py
b/crunch_scripts/split-fastq.py
index be37f043f3859c715f1cfa668173bb2246b7da10..17aabf2930393a48d3539483d5198cab5af35631 100755
(executable)
--- a/
crunch_scripts/split-fastq.py
+++ b/
crunch_scripts/split-fastq.py
@@
-94,7
+94,7
@@
prog = re.compile(r'(.*?)(_[12])?\.fastq(\.gz)?$')
for s in inp.all_streams():
for f in s.all_files():
name_pieces = prog.match(f.name())
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
if s.name() != ".":
# The downstream tool (run-command) only iterates over the top
# level of directories so if there are fastq files in
@@
-105,7
+105,7
@@
for s in inp.all_streams():
sys.exit(1)
p = None
sys.exit(1)
p = None
- if name_pieces.group(2)
!=
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)]
if name_pieces.group(2) == "_1":
p = [{}, {}]
p[0]["reader"] = s.files()[name_pieces.group(0)]
@@
-114,15
+114,16
@@
for s in inp.all_streams():
p = [{}]
p[0]["reader"] = s.files()[name_pieces.group(0)]
p = [{}]
p[0]["reader"] = s.files()[name_pieces.group(0)]
- if p
!=
None:
+ if p
is not
None:
if chunking:
splitfastq(p)
else:
for i in xrange(0, len(p)):
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]])
+ m = p[i]["reader"].as_manifest().split()
+ m[0] = "./_" + str(piece)
+ manifest_list.append(m)
piece += 1
piece += 1
-manifest_text = "\n".join(" ".join(m) for m in manifest_list)
+manifest_text = "\n".join(" ".join(m) for m in manifest_list)
+ "\n"
arvados.current_task().set_output(manifest_text)
arvados.current_task().set_output(manifest_text)