Update v1.2

README.md

@@ -97,7 +97,7 @@ Once installed, you need to indicate the paths to the directory containing the e
 
 #### BLAST
 
-Given that MitoFinder uses makeblastdb, blastn, and blastx, you need to download the associated binaries (latest versions [here](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/)).
+Given that MitoFinder uses makeblastdb, blastn, and blastx, you need to download the associated binaries (latest versions here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/).
 
 ```shell
 wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.0+-x64-macosx.tar.gz 
@@ -243,14 +243,15 @@ optional arguments:
                         Maximum number of codon steps to be tested on each
                         size of the gene to find the start and stop codon
                         during the annotation step. Default = 200 (600 bases)
-  --override            This option tells MitoFinder to override the previous
+  --override            This option forces MitoFinder to override the previous
                         output directory for the selected assembler.
   --ignore              This option tells MitoFinder to ignore the non-
                         standart mitochondrial genes.
   --new-genes           This option tells MitoFinder to try to annotate the
-                        non-standart mitochondrial genes. If several
-                        references are used, make sure the non-standart genes
-                        have the same names in the several references
+                        non-standard animal mitochondrial genes (e.g. rps3 in
+                        fungi). If several references are used, make sure the
+                        non-standard genes have the same names in the several
+                        references
   --allow-intron        This option tells MitoFinder to search for genes with
                         introns. Recommendation : Use it on mitochondrial
                         contigs previously found with MitoFinder without this
@@ -434,7 +435,7 @@ The directory path correponds to the path where the [Seq_ID]_mtDNA_contig.fasta
 
 ### Command line to run tbl2asn
 
-Once your FASTA and TBL files have been created, you can run [tbl2asn](https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/) (download [here](ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/)) as follows:
+Once your FASTA and TBL files have been created, you can run [tbl2asn](https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/) (download here: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/) as follows:
 
 ```shell 
 tbl2asn -t template.sbt -i [Seq_ID].fsa -V v -w assembly.cmt -a s

mitofinder

@@ -83,9 +83,9 @@ if __name__ == "__main__":
 						default=0.00001, dest='blasteVal')
 	parser.add_argument('-n', '--nwalk', help='Maximum number of codon steps to be tested on each size of the gene to find the start and stop codon during the annotation step. Default = 200 (600 bases)', type=int,
 						default=200, dest='nWalk')
-	parser.add_argument('--override', help='This option tells MitoFinder to override the previous output directory for the selected assembler.', default=False, dest='override', action='store_true')
+	parser.add_argument('--override', help='This option forces MitoFinder to override the previous output directory for the selected assembler.', default=False, dest='override', action='store_true')
 	parser.add_argument('--ignore', help='This option tells MitoFinder to ignore the non-standart mitochondrial genes.', default=False, dest='ignore', action='store_true')
-	parser.add_argument('--new-genes', help='This option tells MitoFinder to try to annotate the non-standart mitochondrial genes. If several references are used, make sure the non-standart genes have the same names in the several references', default=False, dest='newG', action='store_true')
+	parser.add_argument('--new-genes', help='This option tells MitoFinder to try to annotate the non-standard animal mitochondrial genes (e.g. rps3 in fungi). If several references are used, make sure the non-standard genes have the same names in the several references', default=False, dest='newG', action='store_true')
 	parser.add_argument('--allow-intron', help='This option tells MitoFinder to search for genes with introns. Recommendation : Use it on mitochondrial contigs previously found with MitoFinder without this option.', default=False, dest='gap', action='store_true')
 	parser.add_argument('--numt', help='This option tells MitoFinder to search for NUMTs. Recommendation : Use it on nuclear contigs previously found with MitoFinder without this option.', default=False, dest='numt', action='store_true')
 	parser.add_argument('--intron-size', help='Size of intron allowed. Default = 1000 bp',
@@ -1047,7 +1047,7 @@ if __name__ == "__main__":
 			print ''
 			print 'MitoFinder found '+str(fl)+' contigs matching provided mitochondrial reference(s)'
 			print 'Did not check for circularization'
-			logfile.write('\nMitofinder found '+str(fl)+' contigs matching provided mitochondrial reference(s)'+'\nDid not check for circularization\n')	
+			logfile.write('\nMitoFinder found '+str(fl)+' contigs matching provided mitochondrial reference(s)'+'\nDid not check for circularization\n')	
 			"""#choose best reference for each contig
 			
 			blastout=open(pathtowork+"/"+args.processName+'_blast_out.txt')