MAINT: Code formatting

graphbin2

@@ -2,12 +2,12 @@
 
 """graphbin2: Refined and overlapped binning of metagenomic contigs using assembly graphs."""
 
-import click
-import os
-import sys
 import logging
+import sys
+
+import click
 
-from src import (graphbin2_SPAdes, graphbin2_SGA, graphbin2_Flye)
+from src import graphbin2_Flye, graphbin2_SGA, graphbin2_SPAdes
 
 __author__ = "Vijini Mallawaarachchi, Anuradha Wickramarachchi, and Yu Lin"
 __copyright__ = "Copyright 2020, GraphBin2 Project"

setup.py

@@ -2,7 +2,6 @@
 
 import setuptools
 
-
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
@@ -30,7 +29,7 @@
     entry_points={
         "console_scripts": [
             "gfa2fasta=src.support.gfa2fasta:main",
-            "prep_result=src.support.prepResult:main"
+            "prep_result=src.support.prepResult:main",
         ],
     },
     classifiers=[

src/bidirectionalmap/bidirectionalmap.py

@@ -6,6 +6,7 @@
 answered by user jme
 """
 
+
 class BidirectionalError(Exception):
     """Must set a unique value in a BijectiveMap."""
 
@@ -38,4 +39,4 @@ def _del_item(self, key):
         super().__delitem__(key)
 
     def _set_item(self, key, value):
-        super().__setitem__(key, value)
+        super().__setitem__(key, value)

src/graph_utils.py

@@ -1,8 +1,10 @@
 import re
 
 from Bio import SeqIO
+
 from .bidirectionalmap.bidirectionalmap import BidirectionalMap
 
+
 def get_contig_lengths_spades(contigs_file):
     # Get length and coverage of contigs
     contig_lengths = {}
@@ -11,26 +13,25 @@ def get_contig_lengths_spades(contigs_file):
     my_map = BidirectionalMap()
 
     for index, record in enumerate(SeqIO.parse(contigs_file, "fasta")):
-        start = 'NODE_'
-        end = '_length'
-        contig_num = int(re.search('%s(.*)%s' % (start, end), record.id).group(1))
-        
-        start = '_length_'
-        end = '_cov'
-        length = int(re.search('%s(.*)%s' % (start, end), record.id).group(1))
-        
-        start = '_cov_'
-        end = ''
-        coverage = int(float(re.search('%s(.*)%s' % (start, end), record.id).group(1)))
-        
+        start = "NODE_"
+        end = "_length"
+        contig_num = int(re.search("%s(.*)%s" % (start, end), record.id).group(1))
+
+        start = "_length_"
+        end = "_cov"
+        length = int(re.search("%s(.*)%s" % (start, end), record.id).group(1))
+
+        start = "_cov_"
+        end = ""
+        coverage = int(float(re.search("%s(.*)%s" % (start, end), record.id).group(1)))
+
         contig_lengths[contig_num] = length
         coverages[contig_num] = coverage
 
     return contig_lengths, coverages
 
 
 def get_contig_paths_spades(contig_paths):
-
     paths = {}
     segment_contigs = {}
     node_count = 0
@@ -44,34 +45,33 @@ def get_contig_paths_spades(contig_paths):
     with open(contig_paths) as file:
         name = file.readline()
         path = file.readline()
-        
+
         while name != "" and path != "":
-
             while ";" in path:
-                path = path[:-2]+","+file.readline()
-            
-            start = 'NODE_'
-            end = '_length_'
-            contig_num = str(int(re.search('%s(.*)%s' % (start, end), name).group(1)))
-            
+                path = path[:-2] + "," + file.readline()
+
+            start = "NODE_"
+            end = "_length_"
+            contig_num = str(int(re.search("%s(.*)%s" % (start, end), name).group(1)))
+
             segments = path.rstrip().split(",")
 
             if current_contig_num != contig_num:
                 my_map[node_count] = int(contig_num)
                 contig_names[node_count] = name.strip()
                 current_contig_num = contig_num
                 node_count += 1
-            
+
             if contig_num not in paths:
                 paths[contig_num] = [segments[0], segments[-1]]
-            
+
             for segment in segments:
                 if segment not in segment_contigs:
                     segment_contigs[segment] = set([contig_num])
                 else:
                     segment_contigs[segment].add(contig_num)
-            
+
             name = file.readline()
             path = file.readline()
 
-    return my_map, 
+    return (my_map,)