--- a/prokka.py	Tue Sep 10 13:11:26 2013 -0400
+++ b/prokka.py	Thu Sep 26 12:39:52 2013 -0400
@@ -21,15 +21,16 @@
     parser.add_option('--mincontig', dest='mincontig', type='int', help='Minimun contig size')
     parser.add_option('--rfam', action="store_true", dest="rfam", help="Enable searching for ncRNAs")
     parser.add_option('--centre', dest="centre", default="CRS4", help="Sequencing centre")
-    parser.add_option('--gff', dest="gff", help="This is the master annotation in GFF3 format, containing both sequences and annotations. It can be viewed directly in Artemis or IGV")
-    parser.add_option('--gbk', dest="gbk", help="This is a standard Genbank file derived from the master .gff. If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, with one record for each sequence")
+    parser.add_option('--gff', dest="gff", help="This is the master annotation in GFF3 format, containing both sequences and annotations")
+    parser.add_option('--gbk', dest="gbk", help="This is a standard GenBank file derived from the master .gff. If the input to prokka was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence")
     parser.add_option('--fna', dest="fna", help="Nucleotide FASTA file of the input contig sequences")
     parser.add_option('--faa', dest="faa", help="Protein FASTA file of the translated CDS sequences")
     parser.add_option('--ffn', dest="ffn", help="Nucleotide FASTA file of all the annotated sequences, not just CDS")
-    parser.add_option('--sqn', dest="sqn", help="An ASN1 format Sequin file for submission to Genbank. It needs to be edited to set the correct taxonomy, authors, related publication etc")
+    parser.add_option('--sqn', dest="sqn", help="An ASN1 format Sequin file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.")
     parser.add_option('--fsa', dest="fsa", help="Nucleotide FASTA file of the input contig sequences, used by tbl2asn to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines")
     parser.add_option('--tbl', dest="tbl", help="Feature Table file, used by tbl2asn to create the .sqn file")
     parser.add_option('--err', dest="err", help="Unacceptable annotations - the NCBI discrepancy report")
+    parser.add_option('--txt', dest='txt', help='Statistics relating to the annotated features found')
     parser.add_option('--log', dest="log", help="Contains all the output that Prokka produced during its run")
     (options, args) = parser.parse_args()
     if len(args) > 0:
@@ -39,9 +40,9 @@
     cpus = "--cpus %d" % (options.cpus) if options.cpus is not None else ''
     rfam = '--rfam' if options.rfam else ''
     mincontig = "--mincontig %d" % options.mincontig if options.mincontig is not None else ''
-    
+
     cl = "prokka --force --outdir . --prefix prokka --kingdom %s %s --centre %s %s %s %s" % (options.kingdom, mincontig, options.centre, rfam, cpus, options.fasta)
-    print '\nProkka command to be executed: \n %s' % cl
+    print '\nProkka command to be executed:\n %s' % cl
 
     # Run command
     log = open(options.log, 'w') if options.log else sys.stdout
@@ -50,11 +51,11 @@
     finally:
         if log != sys.stdout:
             log.close()
-    
+
     # Rename output files
-    suffix = ['gbk', 'fna', 'faa', 'ffn', 'sqn', 'fsa', 'tbl', 'err', 'gff']
+    suffix = ['gff', 'gbk', 'fna', 'faa', 'ffn', 'sqn', 'fsa', 'tbl', 'err', 'txt']
     for s in suffix:
-        shutil.move( 'prokka.' + s, getattr(options, s))
+        shutil.move('prokka.' + s, getattr(options, s))
 
 if __name__ == "__main__":
     __main__()