Added version string and report it in log

README.md

@@ -190,12 +190,12 @@ After stage 2 has been successfully completed, binned assembly contigs can be fo
 #### Clustering result
 The most portable format of the clustering result is `clustering.mcl` which follows the format established by MCL (surprisingly). In this format, each line pertains to a cluster (counting from 1), while the contents of a line is a space-separated list of member sequences.
 
-Therefore a file with the contents:
+E.g. For a MCL file of three lines with the following contents:
 
 ```
-seq1 seq4 seq5
-seq3
-seq2
+L1: seq1 seq4 seq5
+L2: seq2
+L3: seq2
 ```
 
 There are 3 clusters, with memberships as follows:

bin3C.py

@@ -6,13 +6,19 @@
 import logging
 import sys
 
+__version__ = '0.1'
+
 if __name__ == '__main__':
     import argparse
 
+    def mk_version():
+        return 'bin3C v{}'.format(__version__)
+
     def out_name(base, suffix):
         return '{}{}'.format(base, suffix)
 
     global_parser = argparse.ArgumentParser(add_help=False)
+    global_parser.add_argument('-V', '--version', help='Show the application version')
     global_parser.add_argument('-v', '--verbose', default=False, action='store_true', help='Verbose output')
     global_parser.add_argument('--clobber', default=False, action='store_true', help='Clobber existing files')
     global_parser.add_argument('--log', help='Log file path [OUTDIR/bin3C.log]')
@@ -75,6 +81,10 @@ def out_name(base, suffix):
 
     args = parser.parse_args()
 
+    if args.version:
+        print mk_version()
+        sys.exit(0)
+
     try:
         make_dir(args.OUTDIR, args.clobber)
     except IOError as e:
@@ -110,6 +120,10 @@ def out_name(base, suffix):
     fh.setFormatter(formatter)
     root.addHandler(fh)
 
+    # Add some environmental details
+    logger.debug(mk_version())
+    logger.debug(sys.version.replace('\n', ' '))
+
     try:
 
         if args.command == 'mkmap':