Minor refactors and fixing error messages

.gitignore

@@ -1,5 +1,6 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
+*/**/__pycache__/
 *.py[cod]
 *$py.class
 

bin/graphbin → graphbin

@@ -6,7 +6,7 @@ import argparse
 import os
 import sys
 
-from graphbin import (
+from graphbin_utils import (
     graphbin_Options,
     graphbin_Canu,
     graphbin_Flye,
@@ -44,6 +44,7 @@ def main():
         "--assembler",
         type=str,
         help="name of the assembler used (SPAdes, SGA or MEGAHIT). GraphBin supports Flye, Canu and Miniasm long-read assemblies as well.",
+        default=""
     )
     parser.add_argument(
         "--paths",
@@ -61,6 +62,9 @@ def main():
     # Validation of inputs
     # ---------------------------------------------------
     # Check assembler type
+    if len(sys.argv)==1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
     if not (
         args.assembler.lower() == "spades"
         or args.assembler.lower() == "sga"
@@ -72,31 +76,36 @@ def main():
         print(
             "\nPlease make sure to provide the correct assembler type (SPAdes, SGA or MEGAHIT). GraphBin supports Flye, Canu and Miniasm long-read assemblies as well."
         )
-        print("Exiting GraphBin...\nBye...!\n")
+
+        print("\nExiting GraphBin...\nBye...!\n")
         sys.exit(1)
 
     # Check assembly graph file
     if not os.path.isfile(args.graph):
         print("\nFailed to open the assembly graph file.")
-        print("Exiting GraphBin...\nBye...!\n")
+
+        print("\nExiting GraphBin...\nBye...!\n")
         sys.exit(1)
 
     # Check if paths files is provided when the assembler type is SPAdes
     if args.assembler.lower() == "spades" and args.paths is None:
         print("\nPlease make sure to provide the path to the contigs.paths file.")
-        print("Exiting GraphBin...\nBye...!\n")
+
+        print("\nExiting GraphBin...\nBye...!\n")
         sys.exit(1)
 
     # Check contigs.paths file for SPAdes
     if args.assembler.lower() == "spades" and not os.path.isfile(args.paths):
         print("\nFailed to open the contigs.paths file.")
-        print("Exiting GraphBin...\nBye...!\n")
+
+        print("\nExiting GraphBin...\nBye...!\n")
         sys.exit(1)
 
     # Check the file with the initial binning output
     if not os.path.isfile(args.binned):
         print("\nFailed to open the file with the initial binning output.")
-        print("Exiting GraphBin...\nBye...!\n")
+
+        print("\nExiting GraphBin...\nBye...!\n")
         sys.exit(1)
 
     # Handle for missing trailing forwardslash in output folder path
@@ -114,13 +123,15 @@ def main():
     # Validate max_iteration
     if args.max_iteration <= 0:
         print("\nPlease enter a valid number for max_iteration")
-        print("Exiting GraphBin...\nBye...!\n")
+
+        print("\nExiting GraphBin...\nBye...!\n")
         sys.exit(1)
 
     # Validate diff_threshold
     if args.diff_threshold < 0:
         print("\nPlease enter a valid number for diff_threshold")
-        print("Exiting GraphBin...\nBye...!\n")
+
+        print("\nExiting GraphBin...\nBye...!\n")
         sys.exit(1)
 
     # Run GraphBin

graphbin/bidirectionalmap/bidirectionalmap.py → graphbin_utils/bidirectionalmap/bidirectionalmap.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """
 This code is used from the source found at 

graphbin/graphbin_Canu.py → graphbin_utils/graphbin_Canu.py

@@ -22,10 +22,10 @@
 import logging
 
 from igraph import *
-from graphbin.labelpropagation.labelprop import LabelProp
-from graphbin.bidirectionalmap.bidirectionalmap import BidirectionalMap
-from graphbin.graphbin_Func import getClosestLabelledVertices
-from graphbin.graphbin_Options import PARSER
+from graphbin_utils.labelpropagation.labelprop import LabelProp
+from graphbin_utils.bidirectionalmap.bidirectionalmap import BidirectionalMap
+from graphbin_utils.graphbin_Func import getClosestLabelledVertices
+from graphbin_utils.graphbin_Options import PARSER
 
 # Sample command
 # -------------------------------------------------------------------

graphbin/graphbin_Flye.py → graphbin_utils/graphbin_Flye.py

@@ -22,10 +22,10 @@
 import logging
 
 from igraph import *
-from graphbin.labelpropagation.labelprop import LabelProp
-from graphbin.bidirectionalmap.bidirectionalmap import BidirectionalMap
-from graphbin.graphbin_Func import getClosestLabelledVertices
-from graphbin.graphbin_Options import PARSER
+from graphbin_utils.labelpropagation.labelprop import LabelProp
+from graphbin_utils.bidirectionalmap.bidirectionalmap import BidirectionalMap
+from graphbin_utils.graphbin_Func import getClosestLabelledVertices
+from graphbin_utils.graphbin_Options import PARSER
 
 
 # Sample command

graphbin/graphbin_MEGAHIT.py → graphbin_utils/graphbin_MEGAHIT.py

@@ -22,10 +22,10 @@
 import logging
 
 from igraph import *
-from graphbin.labelpropagation.labelprop import LabelProp
-from graphbin.bidirectionalmap.bidirectionalmap import BidirectionalMap
-from graphbin.graphbin_Func import getClosestLabelledVertices
-from graphbin.graphbin_Options import PARSER
+from graphbin_utils.labelpropagation.labelprop import LabelProp
+from graphbin_utils.bidirectionalmap.bidirectionalmap import BidirectionalMap
+from graphbin_utils.graphbin_Func import getClosestLabelledVertices
+from graphbin_utils.graphbin_Options import PARSER
 
 # Sample command
 # -------------------------------------------------------------------

graphbin/graphbin_Miniasm.py → graphbin_utils/graphbin_Miniasm.py

@@ -22,10 +22,10 @@
 import logging
 
 from igraph import *
-from graphbin.labelpropagation.labelprop import LabelProp
-from graphbin.bidirectionalmap.bidirectionalmap import BidirectionalMap
-from graphbin.graphbin_Func import getClosestLabelledVertices
-from graphbin.graphbin_Options import PARSER
+from graphbin_utils.labelpropagation.labelprop import LabelProp
+from graphbin_utils.bidirectionalmap.bidirectionalmap import BidirectionalMap
+from graphbin_utils.graphbin_Func import getClosestLabelledVertices
+from graphbin_utils.graphbin_Options import PARSER
 
 
 # Sample command

graphbin/graphbin_SGA.py → graphbin_utils/graphbin_SGA.py

@@ -22,10 +22,10 @@
 import logging
 
 from igraph import *
-from graphbin.labelpropagation.labelprop import LabelProp
-from graphbin.bidirectionalmap.bidirectionalmap import BidirectionalMap
-from graphbin.graphbin_Func import getClosestLabelledVertices
-from graphbin.graphbin_Options import PARSER
+from graphbin_utils.labelpropagation.labelprop import LabelProp
+from graphbin_utils.bidirectionalmap.bidirectionalmap import BidirectionalMap
+from graphbin_utils.graphbin_Func import getClosestLabelledVertices
+from graphbin_utils.graphbin_Options import PARSER
 
 
 # Sample command

graphbin/graphbin_SPAdes.py → graphbin_utils/graphbin_SPAdes.py

@@ -24,10 +24,10 @@
 from igraph import *
 from collections import defaultdict
 
-from graphbin.labelpropagation.labelprop import LabelProp
-from graphbin.bidirectionalmap.bidirectionalmap import BidirectionalMap
-from graphbin.graphbin_Func import getClosestLabelledVertices
-from graphbin.graphbin_Options import PARSER
+from graphbin_utils.labelpropagation.labelprop import LabelProp
+from graphbin_utils.bidirectionalmap.bidirectionalmap import BidirectionalMap
+from graphbin_utils.graphbin_Func import getClosestLabelledVertices
+from graphbin_utils.graphbin_Options import PARSER
 
 # Sample command
 # -------------------------------------------------------------------

graphbin/labelpropagation/labelprop.py → graphbin_utils/labelpropagation/labelprop.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """
 This code has been modified from the source found at https://github.com/ZwEin27/python-labelpropagation

setup.py

@@ -1,17 +1,17 @@
 #!/usr/bin/env python3
 
 import os
-from setuptools import setup
+from setuptools import setup, find_packages
 
 with open("README.md") as f:
     long_description = f.read()
 
-packages = ["graphbin"]
+packages = find_packages()
 package_data = {
-    "graphbin": [
-        "graphbin/*.py",
-        "graphbin/bidirectionalmap/*.py",
-        "graphbin/labelpropagation/*.py",
+    "graphbin_utils": [
+        "graphbin_utils/*.py",
+        "graphbin_utils/bidirectionalmap/*.py",
+        "graphbin_utils/labelpropagation/*.py",
     ]
 }
 data_files = [(".", ["LICENSE", "README.md"])]
@@ -25,7 +25,7 @@
     package_data=package_data,
     data_files=data_files,
     include_package_data=True,
-    scripts=['bin/graphbin'],
+    scripts=['graphbin'],
     url='https://github.com/Vini2/graphbin',
     license='GPLv2',
     long_description_content_type="text/markdown",