X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/efd131427759f5a2663dea04a402054e361b7c90..a3787ef83a0538097fb6f802f675be740a241ebc:/crunch_scripts/split-fastq.py

diff --git a/crunch_scripts/split-fastq.py b/crunch_scripts/split-fastq.py
index 8b80adf635..17aabf2930 100755
--- 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())
-        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
@@ -104,7 +104,8 @@ for s in inp.all_streams():
                 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)]
@@ -113,14 +114,16 @@ for s in inp.all_streams():
                 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)