Be more flexible with fastq filenames.

Allow pass/nopass, all, or no filter flag.

Also add more information to exception text

diff --git a/htsworkflow/pipelines/sequences.py b/htsworkflow/pipelines/sequences.py
index 627dfe3667a8500bd9132aba635221d150d81bbe..84bafbfb4af38d95aa68e25083650747d0c73df4 100644 (file)
--- a/htsworkflow/pipelines/sequences.py
+++ b/htsworkflow/pipelines/sequences.py
@@ -116,7 +116,9 @@ def get_flowcell_cycle(path):
     rest, flowcell = os.path.split(rest)
     cycle_match = re.match("C(?P<start>[0-9]+)-(?P<stop>[0-9]+)", cycle)
     if cycle_match is None:
-        raise ValueError("Expected .../flowcell/cycle/ directory structure")
+        raise ValueError(
+            "Expected .../flowcell/cycle/ directory structure in %s" % \
+            (path,))
     start = cycle_match.group('start')
     if start is not None:
         start = int(start)
@@ -156,6 +158,8 @@ def parse_qseq(path, filename):
     return SequenceFile('qseq', fullpath, flowcell, lane, read, cycle=stop)
 
 def parse_fastq(path, filename):
+    """Parse fastq names
+    """
     flowcell_dir, start, stop = get_flowcell_cycle(path)
     basename, ext = os.path.splitext(filename)
     records = basename.split('_')
@@ -163,19 +167,33 @@ def parse_fastq(path, filename):
     flowcell = records[4]
     lane = int(records[5][1])
     read = int(records[6][1])
-    if records[-1].startswith('pass'):
-        pf = True
-    elif records[-1].startswith('nopass'):
-        pf = False
-    else:
-        raise ValueError("Unrecognized fastq name")
-        
+    pf = parse_fastq_pf_flag(records)
+    
     if flowcell_dir != flowcell:
         logging.warn("flowcell %s found in wrong directory %s" % \
                          (flowcell, path))
 
     return SequenceFile('fastq', fullpath, flowcell, lane, read, pf=pf, cycle=stop)
 
+def parse_fastq_pf_flag(records):
+    """Take a fastq filename split on _ and look for the pass-filter flag
+    """
+    if len(records) < 8:
+        pf = None
+    else:
+        fastq_type = records[-1].lower()
+        if fastq_type.startswith('pass'):
+            pf = True
+        elif fastq_type.startswith('nopass'):
+            pf = False
+        elif fastq_type.startswith('all'):
+            pf = None
+        else:
+            raise ValueError("Unrecognized fastq name %s at %s" % \
+                             (records[-1], os.path.join(path,filename)))
+
+    return pf
+    
 def parse_eland(path, filename, eland_match=None):
     if eland_match is None:
         eland_match = eland_re.match(filename)