Linting

BLAST/configure.py

@@ -3,7 +3,7 @@
 """Write and parse configuration files for BLASTn"""
 
 import sys
-if sys.version_info.major is not 3:
+if sys.version_info.major != 3:
     sys.exit("Please use Python 3 for this module: " + __name__)
 
 import configparser

BLAST/runblastn.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import sys
-if sys.version_info.major is not 3:
+if sys.version_info.major != 3:
     sys.exit("Please use Python 3 for this module: " + __name__)
 
 import os

Objects/alignment.py

@@ -1,11 +1,13 @@
 #!/usr/bin/env python3
 
 import sys
-if sys.version_info.major is not 3:
+
+if sys.version_info.major != 3:
     sys.exit("Please use Python 3 for this module: " + __name__)
 
 import re
 
+
 #   A class definition for a SAM alignment
 class Alignment(object):
     """A class to hold a SAM Alignment
@@ -16,27 +18,35 @@ class Alignment(object):
         1-based leftmost mapping position
         Cigar string
     """
-    _CIGAR = re.compile(u'([0-9]+[A-Z]+)') # Regex to break the CIGAR string into component codes using re.findall()
+
+    _CIGAR = re.compile(
+        "([0-9]+[A-Z]+)"
+    )  # Regex to break the CIGAR string into component codes using re.findall()
+
     def __init__(self, line):
         try:
             assert isinstance(line, str)
         except AssertionError:
             raise TypeError
         #   There's only some information that we need for our alignment, everything else is forgotten
-        split_line = line.strip().split() # Remove leading and trailing whitespace, then split the line by column
-        self._qname = split_line[0] # First column in a SAM file
-        self._flag = int(split_line[1]) # Second column
-        self._rname = split_line[2] # Third column
-        self._pos = int(split_line[3]) # Fourth column, should be an int
-        self._cigar = self._CIGAR.findall(split_line[5]) # Sixth column, after breaking up the CIGAR string into a list of component codes
+        split_line = (
+            line.strip().split()
+        )  # Remove leading and trailing whitespace, then split the line by column
+        self._qname = split_line[0]  # First column in a SAM file
+        self._flag = int(split_line[1])  # Second column
+        self._rname = split_line[2]  # Third column
+        self._pos = int(split_line[3])  # Fourth column, should be an int
+        self._cigar = self._CIGAR.findall(
+            split_line[5]
+        )  # Sixth column, after breaking up the CIGAR string into a list of component codes
 
     def __repr__(self):
-        return self._rname + ':' + self._qname
+        return self._rname + ":" + self._qname
 
     def get_rc(self):
         """Check to see if we're reverse complementing our sequence"""
         #   If the 16th bit is set, it's reverse complement
-        return self._flag is 16
+        return self._flag == 16
 
     def get_name(self):
         """Get the alignment name"""
@@ -56,5 +66,4 @@ def get_cigar(self):
 
     def check_flag(self):
         """Make sure we don't have extraneous alignments"""
-        return self._flag is 0 or self._flag is 16
-
+        return self._flag == 0 or self._flag == 16