lint

mxdx/__init__.py

@@ -1,2 +1,4 @@
+"""mxdx: multiplexing and demultiplexing records since the early 90s."""
+
 from . import _version
 __version__ = _version.get_versions()['version']

mxdx/_io.py

@@ -321,7 +321,7 @@ def valid_interleave(cls):
 
     @staticmethod
     def io_from_stream(stream, n_lines=4):
-        """Sniff a datastream which cannot be seeked"""
+        """Sniff a datastream which cannot be seeked."""
         lines = ''.join([stream.readline() for i in range(n_lines)])
         buf = io.StringIO(lines)
         read_f, write_f = IO.sniff(buf)
@@ -370,7 +370,7 @@ def sniff(cls, data):
 
         for fn_read, fn_write in io_pairs:
             buf.seek(0)
-            if next(fn_read(buf)) != None:
+            if next(fn_read(buf)) is not None:
                 return (fn_read, fn_write)
 
         return None, None
@@ -449,30 +449,31 @@ def _readfq(fp): # this is a generator function
     last = None # this is a buffer keeping the last unprocessed line
     while True: # mimic closure; is it a bad idea?
         if not last: # the first record or a record following a fastq
-            for l in fp: # search for the start of the next record
-                if l[0] in '>@': # fasta/q header line
-                    last = l[:-1] # save this line
+            for line in fp: # search for the start of the next record
+                if line[0] in '>@': # fasta/q header line
+                    last = line[:-1] # save this line
                     break
         if not last:
             break
         name, seqs, last = last[1:].partition(" ")[0], [], None
-        for l in fp: # read the sequence
-            if l[0] in '@+>':
-                last = l[:-1]
+        for line in fp: # read the sequence
+            if line[0] in '@+>':
+                last = line[:-1]
                 break
-            seqs.append(l[:-1])
+            seqs.append(line[:-1])
         if not last or last[0] != '+': # this is a fasta record
             yield name, ''.join(seqs), None # yield a fasta record
             count += 1
-            if not last: break
+            if not last:
+                break
         else: # this is a fastq record
             seq, leng, seqs = ''.join(seqs), 0, []
-            for l in fp: # read the quality
-                seqs.append(l[:-1])
-                leng += len(l) - 1
+            for line in fp: # read the quality
+                seqs.append(line[:-1])
+                leng += len(line) - 1
                 if leng >= len(seq): # have read enough quality
                     last = None
-                    yield name, seq, ''.join(seqs); # yield a fastq record
+                    yield name, seq, ''.join(seqs) # yield a fastq record
                     count += 1
                     break
             if last: # reach EOF before reading enough quality
@@ -503,7 +504,7 @@ def _readsam(data):
 
                 if not refstart.isdigit():
                     raise ParseError()
-            except:
+            except:  # noqa E722
                 yield None, None
                 break
             else:

mxdx/_mxdx.py

@@ -16,6 +16,7 @@
 
 class Multiplex:
     """Multiplex records from a file batch."""
+
     def __init__(self, file_map, batch, paired_handling, output):
         self._file_map = file_map
         self._batch = batch
@@ -48,7 +49,7 @@ def _read_sequential(self, r1_reader, r2_reader):
             yield rec
 
     def read(self):
-        """Read requested records, tag them, and emplace in a queue"""
+        """Read requested records, tag them, and emplace in a queue."""
         mode = 'rt'
 
         read_f = self._read_f
@@ -139,6 +140,7 @@ class BufferedQueue:
     To adjust for this, we're increasing the amount of data which an
     individual queue item can hold.
     """
+
     BUFSIZE = 1024
 
     def __init__(self, ctx):
@@ -215,7 +217,7 @@ def start(self):
         writer.join()
 
     def read(self):
-        """Read from the input stream and queue"""
+        """Read from the input stream and queue."""
         # we can't pickle the streams so this has to be thread local
         if self._mux_input == '-':
             # see https://docs.python.org/3/library/multiprocessing.html#programming-guidelines
@@ -267,7 +269,7 @@ def _write_rec(self, mx, rec):
         out_f.write(rec.write())
 
     def write(self):
-        """Write to the respective outputs"""
+        """Write to the respective outputs."""
         default = MuxFile("badtag.r1", "badtag.r2", 0, sys.maxsize, "badtag",
                           False)
 

mxdx/cli.py

@@ -1,3 +1,4 @@
+"""mxdx: multiplexing and demultiplexing."""
 import click
 import sys
 import pathlib
@@ -9,6 +10,7 @@
 
 @click.group()
 def cli():
+    """mxdx: multiplexing and demultiplexing."""
     pass
 
 

setup.py

@@ -1,4 +1,4 @@
-"""mxdx: multiplexing and demultiplexing tools"""
+"""mxdx: multiplexing and demultiplexing."""
 import versioneer
 from setuptools import setup, find_packages