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BigDataBiology · Jun 12, 2020 · 1d1f6ee · 1d1f6ee
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diff --git a/README.md b/README.md
@@ -23,9 +23,9 @@ available for genome mode.
 
 * `-o/--output`: Output directory (will be created if non-existent).
 
-* `-nt_input`: path to the input DNA gene file(.fasta/.gz/.bz2).
+* `--nt_input`: path to the input DNA gene file(.fasta/.gz/.bz2).
 
-* `-aa_input`: path to the input Protein gene file(.fasta/.gz/.bz2).
+* `--aa_input`: path to the input Protein gene file(.fasta/.gz/.bz2).
 
 ## Examples
 
@@ -38,14 +38,14 @@ gmgc-finder -i input.fasta -o output
 2. Input is DNA/protein gene sequences
 
 ```bash
-gmgc-finder -nt_input genes.fna -aa_input genes.faa -o output
+gmgc-finder --nt_input genes.fna --aa_input genes.faa -o output
 ```
 
 The nucleotide input is optional (but should be used if available so that the
 quality of the hits can be refined):
 
 ```bash
-gmgc-finder -aa_input genes.faa -o output
+gmgc-finder --aa_input genes.faa -o output
 ```
 
 If yout input is a metagenome, you can use

diff --git a/docs/usage.md b/docs/usage.md
@@ -6,9 +6,9 @@
 
 * `-o/--output` : Output directory (will be created if non-existent).
 
-* `-nt_input` : path to the input DNA gene file(.fasta/.gz/.bz2).
+* `--nt_input` : path to the input DNA gene file(.fasta/.gz/.bz2).
 
-* `-aa_input` : path to the input Protein gene file(.fasta/.gz/.bz2).
+* `--aa_input` : path to the input Protein gene file(.fasta/.gz/.bz2).
 
 The input must contain a genome file or DNA and Protein gene file or just Protein gene file.
 
@@ -26,10 +26,10 @@ GMGC-finder will call `prodigal` to predict genes and then process each gene.
    respectfully).
 
 ```bash
-gmgc-finder -nt_input genes.fna -aa_input genes.faa -o output
+gmgc-finder --nt_input genes.fna --aa_input genes.faa -o output
 ```
 ```bash
-gmgc-finder -aa_input genes.faa -o output
+gmgc-finder --aa_input genes.faa -o output
 ```
 # Processing metagenomes using NGLess
 

diff --git a/gmgc_finder/main.py b/gmgc_finder/main.py
@@ -32,10 +32,16 @@ def parse_args(args):
                         help='Output directory (will be created if non-existent)',
                         dest='output',
                         default = None)
-    parser.add_argument('-nt_genes',required=False,help = 'Path to the input DNA gene file.',dest='nt_input',
-                        default = None)
-    parser.add_argument('-aa_genes',required=False,help = 'Path to the input Protein gene file.',dest='aa_input',
-                        default = None)
+    parser.add_argument('--nt_genes',
+                        required=False,
+                        help='Path to the input DNA gene file (FASTA format)',
+                        dest='nt_input',
+                        default=None)
+    parser.add_argument('--aa_genes',
+                        required=False,
+                        help='Path to the input amino acid gene file (FASTA format)',
+                        dest='aa_input',
+                        default=None)
     return parser.parse_args()
 
 def gene_prediction(fasta_input,output):