ENH/BUG/MAINT: support comments/blank lines and better validation in "per-sample sequence" formats

q2_types/per_sample_sequences/__init__.py

@@ -10,6 +10,7 @@
 
 from ._format import (CasavaOneEightSingleLanePerSampleDirFmt, FastqGzFormat,
                       YamlFormat, FastqManifestFormat,
+                      FastqAbsolutePathManifestFormat,
                       SingleLanePerSampleSingleEndFastqDirFmt,
                       SingleLanePerSamplePairedEndFastqDirFmt,
                       SingleEndFastqManifestPhred33,
@@ -21,6 +22,7 @@
 
 __all__ = ['CasavaOneEightSingleLanePerSampleDirFmt', 'FastqGzFormat',
            'YamlFormat', 'FastqManifestFormat',
+           'FastqAbsolutePathManifestFormat',
            'SingleLanePerSampleSingleEndFastqDirFmt',
            'SingleLanePerSamplePairedEndFastqDirFmt', 'SequencesWithQuality',
            'PairedEndSequencesWithQuality', 'PerSampleDNAIterators',

q2_types/per_sample_sequences/_format.py

@@ -13,15 +13,74 @@
 from ..plugin_setup import plugin
 
 
-class FastqManifestFormat(model.TextFileFormat):
+class _FastqManifestBase(model.TextFileFormat):
     """
-    Mapping of sample identifiers to filepaths and read direction.
+    Base class for mapping of sample identifiers to filepaths and read
+    direction.
 
     """
+    EXPECTED_HEADER = None
+
     def sniff(self):
         with self.open() as fh:
-            header = fh.readline()
-            return header.strip() == 'sample-id,filename,direction'
+            data_lines = 0
+            header = None
+            while data_lines < 10:
+                line = fh.readline()
+
+                if line == '':
+                    # EOF
+                    break
+                elif line.lstrip(' ') == '\n':
+                    # Blank line
+                    continue
+                elif line.startswith('#'):
+                    # Comment line
+                    continue
+
+                cells = line.rstrip('\n').split(',')
+                if header is None:
+                    if cells != self.EXPECTED_HEADER:
+                        return False
+                    header = cells
+                else:
+                    if len(cells) != len(header):
+                        return False
+                    data_lines += 1
+
+            return header is not None and data_lines > 0
+
+
+class FastqManifestFormat(_FastqManifestBase):
+    """
+    Mapping of sample identifiers to relative filepaths and read direction.
+
+    """
+    EXPECTED_HEADER = ['sample-id', 'filename', 'direction']
+
+
+class FastqAbsolutePathManifestFormat(_FastqManifestBase):
+    """
+    Mapping of sample identifiers to absolute filepaths and read direction.
+
+    """
+    EXPECTED_HEADER = ['sample-id', 'absolute-filepath', 'direction']
+
+
+class SingleEndFastqManifestPhred33(FastqAbsolutePathManifestFormat):
+    pass
+
+
+class SingleEndFastqManifestPhred64(FastqAbsolutePathManifestFormat):
+    pass
+
+
+class PairedEndFastqManifestPhred33(FastqAbsolutePathManifestFormat):
+    pass
+
+
+class PairedEndFastqManifestPhred64(FastqAbsolutePathManifestFormat):
+    pass
 
 
 class YamlFormat(model.TextFileFormat):
@@ -64,40 +123,6 @@ def sniff(self):
         return False
 
 
-class FastqAbsolutePathManifestFormat(model.TextFileFormat):
-    """
-    Mapping of sample identifiers to filepaths and read direction.
-
-    """
-    def sniff(self):
-        expected_header = 'sample-id,absolute-filepath,direction'
-        with self.open() as fh:
-            for line in fh:
-                line = line.strip()
-                if line and not line.startswith('#'):
-                    # the first non-blank, non-comment line should be
-                    # the header
-                    return line == expected_header
-        # never found the header
-        return False
-
-
-class SingleEndFastqManifestPhred33(FastqAbsolutePathManifestFormat):
-    pass
-
-
-class SingleEndFastqManifestPhred64(FastqAbsolutePathManifestFormat):
-    pass
-
-
-class PairedEndFastqManifestPhred33(FastqAbsolutePathManifestFormat):
-    pass
-
-
-class PairedEndFastqManifestPhred64(FastqAbsolutePathManifestFormat):
-    pass
-
-
 class CasavaOneEightSingleLanePerSampleDirFmt(model.DirectoryFormat):
     sequences = model.FileCollection(
         r'.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz',