more delinting

.pylintrc

@@ -4,5 +4,5 @@
 # C0326: Disabled because it incorrectly flags whitespace around default values
 #        when function annotations are used; will add a custom checker that
 #        flags all other cases
-disable=fixme,C0303,C0326,too-few-public-methods,too-many-instance-attributes,too-many-arguments,too-many-locals,too-many-branches,too-many-statements,too-many-function-args,too-many-lines,too-many-boolean-expressions,too-many-return-statements
+disable=fixme,C0303,C0326,too-few-public-methods,too-many-instance-attributes,too-many-arguments,too-many-locals,too-many-branches,too-many-statements,too-many-function-args,too-many-lines,too-many-boolean-expressions,too-many-return-statements,too-many-ancestors
 ignore=__pycache__,*.pyx,_version.py

atropos/commands/trim.py

@@ -5,16 +5,26 @@
 import os
 import sys
 import textwrap
+from atropos import AtroposError
 from atropos.commands import (
     Pipeline, SingleEndPipelineMixin, PairedEndPipelineMixin, create_reader)
 from atropos.commands import load_known_adapters
 from atropos.commands.stats import (
     SingleEndReadStatistics, PairedEndReadStatistics)
 from atropos.adapters import AdapterParser, BACK
 # TODO: Only import used members
-from atropos.trim.modifiers import *
-from atropos.trim.filters import *
-from atropos.trim.writers import *
+from atropos.trim.modifiers import (
+    AdapterCutter, DoubleEncoder, InsertAdapterCutter, LengthTagModifier,
+    MergeOverlapping, MinCutter, NEndTrimmer, NextseqQualityTrimmer,
+    NonDirectionalBisulfiteTrimmer, OverwriteRead, PairedEndModifiers,
+    PrefixSuffixAdder, PrimerTrimmer, QualityTrimmer, RRBSTrimmer,
+    SingleEndModifiers, SuffixRemover, SwiftBisulfiteTrimmer,
+    UnconditionalCutter, ZeroCapper)
+from atropos.trim.filters import (
+    FilterFactory, Filters, MergedReadFilter, NContentFilter, NoFilter,
+    TooLongReadFilter, TooShortReadFilter, TrimmedFilter, UntrimmedFilter)
+from atropos.trim.writers import (
+    Formatters, InfoFormatter, RestFormatter, WildcardFormatter, Writers)
 from atropos.io import STDOUT
 from atropos.util import RandomMatchProbability, Const, run_interruptible
 

atropos/io/progress.py

@@ -149,6 +149,8 @@ def __next__(self):
                 raise
 
         def close(self):
+            """Finish the progress bar and close the underlying iterator.
+            """
             if not self.done:
                 self.finish()
                 self.done = True
@@ -161,6 +163,7 @@ class MagCounter(progressbar.widgets.WidgetBase):
         """Custom widget that formats the value using a specified magnitude.
         """
         def __init__(self, mag_format):
+            super().__init__()
             self._format = mag_format
 
         def __call__(self, progress, data):

atropos/io/seqio.py

@@ -39,9 +39,13 @@ def __init__(self, path, mode='r'):
 
     @property
     def name(self):
+        """The underlying file name.
+        """
         return self._file.name
 
     def close(self):
+        """Close the underlying file.
+        """
         if self._close_on_exit and self._file is not None:
             self._file.close()
             self._file = None
@@ -144,6 +148,8 @@ def __iter__(self):
             yield line
 
     def close(self):
+        """Close the underlying file.
+        """
         self._file.close()
 
 class FastaReader(SequenceReader):
@@ -252,6 +258,8 @@ def __iter__(self):
                 fastaread.name, fastaread.sequence, qualities)
 
     def close(self):
+        """Close the underlying files.
+        """
         self.fastareader.close()
         self.qualreader.close()
 
@@ -341,6 +349,8 @@ def __iter__(self):
             yield (read1, read2)
 
     def close(self):
+        """Close the underlying files.
+        """
         self.reader1.close()
         self.reader2.close()
 
@@ -380,6 +390,8 @@ def __iter__(self):
             yield (read1, read2)
 
     def close(self):
+        """Close the underlying reader.
+        """
         self.reader.close()
 
     def __enter__(self):
@@ -412,13 +424,20 @@ def __iter__(self):
         import pysam
         return self._iter(pysam.AlignmentFile(self._file))
 
+    def _iter(self, sam):
+        """Create an iterator over records in the SAM/BAM file.
+        """
+        raise NotImplementedError()
+
     def __enter__(self):
         return self
 
     def __exit__(self, *args):
         self.close()
 
     def close(self):
+        """Close the underling AlignmentFile.
+        """
         if self._close_on_exit and self._file is not None:
             self._file.close()
             self._file = None
@@ -654,6 +673,8 @@ def format(self, read):
         return self.format_entry(read.name, read.sequence)
 
     def format_entry(self, name, sequence):
+        """Convert a sequence record to a string.
+        """
         if self.text_wrapper:
             sequence = self.text_wrapper.fill(sequence)
         return "".join((">", name, "\n", sequence, "\n"))
@@ -672,6 +693,8 @@ def format(self, read):
             read.name, read.sequence, read.qualities, read.name2)
 
     def format_entry(self, name, sequence, qualities, name2=""):
+        """Convert a sequence record to a string.
+        """
         return "".join((
             '@', name, '\n',
             sequence, '\n+',
@@ -722,8 +745,7 @@ class InterleavedFormatter(SingleEndFormatter):
     def format(self, result, read1, read2=None):
         result[self.file1].extend((
             self.seq_format.format(read1),
-            self.seq_format.format(read2)
-        ))
+            self.seq_format.format(read2)))
         self.written += 1
         self.read1_bp += len(read1)
         self.read2_bp += len(read2)

atropos/scripts/atropos.py

@@ -46,6 +46,11 @@ def __init__(self, *args, **kwargs):
 
     def __call__(self, string):
         return self._do_call(string, *self.args, **self.kwargs) or string
+
+    def _do_call(string, *args, **kwargs):
+        """Convert and/or validate `string`.
+        """
+        raise NotImplementedError()
 
 class CompositeType(object):
     """A composite of multiple data types.
@@ -211,6 +216,8 @@ def between(min_val=None, max_val=None, type_=int):
 
 class Command(object):
     """Base class for Atropos sub-commands.
+    
+    Subclasses must define name, description, and usage members.
     """
     def __init__(self, args):
         self.orig_args = copy.copy(args)