X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/363d128327963a7c1d93992613a741af4d5f55fd..1b8d669706fb952f0e5d1ad5e407073f4815907f:/crunch_scripts/split-fastq.py

diff --git a/crunch_scripts/split-fastq.py b/crunch_scripts/split-fastq.py
index a279198742..1c7a36871d 100755
--- a/crunch_scripts/split-fastq.py
+++ b/crunch_scripts/split-fastq.py
@@ -3,6 +3,7 @@
 import arvados
 import re
 import hashlib
+import string
 
 api = arvados.api('v1')
 
@@ -13,89 +14,54 @@ manifest_text = ""
 
 inp = arvados.CollectionReader(arvados.getjobparam('reads'))
 
-prog = re.compile(r'(.*?)_1.fastq(.gz)?$')
+manifest_list = []
 
-manifest_text = ""
-
-def readline(reader, start):
-    line = ""
+def nextline(reader, start):
     n = -1
-    while n == -1:
-        r = reader.readfrom(start, 1024)
+    while True:
+        r = reader.readfrom(start, 128)
         if r == '':
             break
         n = string.find(r, "\n")
-        line += r[0:n]
-        start += len(r)
-    return line
-
-def splitfastq(p):
-    for i in xrange(0, len(p)):
-        p[i]["start"] = 0
-        p[i]["end"] = 0
-
-    while True:
-        recordsize = [0, 0]
-
-        # read 4 lines starting at "start"
-        for ln in xrange(0, 4):
-            for i in xrange(0, len(p)):
-                r = readline(p[i]["reader"], p[i]["start"])
-                if r == '':
-                    return
-                recordsize[i] += len(r)
-
-        splitnow = False
-        for i in xrange(0, len(p)):
-            if ((p[i]["end"] - p[i]["start"]) + recordsize[i]) >= arvados.BLOCKSIZE:
-                splitnow = True
-
-        if splitnow:
-            for i in xrange(0, len(p)):
-                global piece
-                global manifest_text
-                manifest = []
-                manifest.extend("./_" + str(piece))
-                manifest.extend([d[LOCATOR] for d in p["reader"]._stream._data_locators])
-                manifest.extend(["{}:{}:{}".format(seg[LOCATOR], seg[BLOCKSIZE], self.name().replace(' ', '\\040')) for seg in arvados.locators_and_ranges(p[i]["reader"].segments, p[i]["start"], p[i]["end"] - p[i]["start"])])
-                manifest_text += manifest.join(" ") + "\n"
-                p[i]["start"] = p[i]["end"]
+        if n > -1:
+            break
         else:
-            for i in xrange(0, len(p)):
-                p[i]["end"] += recordsize[i]
+            start += 128
+    return n
 
+prog = re.compile(r'(.*?)(_[12])?\.fastq(\.gz)?$')
 
+# Look for fastq files
 for s in inp.all_streams():
-    if s.name() == ".":
-        for f in s.all_files():
-            result = prog.match(f.name())
-            if result != None:
-                p = [{}, {}]
-                p[0]["reader"] = s.files()[result.group(0)]
-                if result.group(2) != None:
-                    p[1]["reader"] = s.files()[result.group(1) + "_2.fastq" + result.group(2)]
-                else:
-                    p[1]["reader"] = s.files()[result.group(1) + "_2.fastq"
-                splitfastq(p)
-                #m0 = p[0]["reader"].as_manifest()[1:]
-                #m1 = p[1]["reader"].as_manifest()[1:]
-                #manifest_text += "./_" + str(piece) + m0
-                #manifest_text += "./_" + str(piece) + m1
+    for f in s.all_files():
+        name_pieces = prog.match(f.name())
+        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
+                # directories in the input, the choice is either to forget
+                # there are directories (which might lead to name conflicts) or
+                # just fail.
+                print >>sys.stderr, "fastq must be at the root of the collection"
+                sys.exit(1)
+
+            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[1]["reader"] = s.files()[name_pieces.group(1) + "_2.fastq" + (name_pieces.group(3) if name_pieces.group(3) else '')]
+            else:
+                p = [{}]
+                p[0]["reader"] = s.files()[name_pieces.group(0)]
+
+            if p is not None:
+                for i in xrange(0, len(p)):
+                    m = p[i]["reader"].as_manifest().split()
+                    m[0] = "./_" + str(piece)
+                    manifest_list.append(m)
                 piece += 1
 
-# No pairs found so just put each fastq file into a separate directory
-if manifest_text == "":
-    for s in inp.all_streams():
-        prog = re.compile("(.*?).fastq(.gz)?$")
-        if s.name() == ".":
-            for f in s.all_files():
-                result = prog.match(f.name())
-                if result != None:
-                    p = [{}]
-                    p[0]["reader"] = s.files()[result.group(0)]
-                    splitfastq(p)
-                    #m0 = p[0]["reader"].as_manifest()[1:]
-                    #manifest_text += "./_" + str(piece) + m0
-                    piece += 1
+manifest_text = "\n".join(" ".join(m) for m in manifest_list) + "\n"
 
 arvados.current_task().set_output(manifest_text)