diff --git a/metaSNV_post.py b/metaSNV_post.py index 97796a9c418266b2853426e8412dc9c774d01ef9..656e34d3902a88ed50f337aad4a3ecd15343b617 100755 --- a/metaSNV_post.py +++ b/metaSNV_post.py @@ -43,8 +43,10 @@ def get_arguments(): # OPTIONAL arguments: - parser.add_argument('-b', metavar='FLOAT', type=float, help="Coverage breadth: Horizontal genome coverage percentage per sample per species", default=40.0) - parser.add_argument('-d', metavar='FLOAT', type=float, help="Coverage depth: Average vertical genome coverage per sample per species", default=5.0) + parser.add_argument('-b', metavar='FLOAT', type=float, default=40.0) + help="Coverage breadth: minimal horizontal genome coverage percentage per sample per species") + parser.add_argument('-d', metavar='FLOAT', type=float, default=5.0, + help="Coverage depth: minimal average vertical genome coverage per sample per species") parser.add_argument('-m',metavar='INT', type=int, help="Minimum number of samples per species", default=2) parser.add_argument('-c',metavar='FLOAT', type=float, help="FILTERING STEP II: minimum coverage per position per sample per species", default=5.0) parser.add_argument('-p',metavar='FLOAT', type=float, help="FILTERING STEP II: required proportion of informative samples (coverage non-zero) per position", default=0.50)