Merge pull request #23 from TCLamnidis/main

removed metavar attributes from argparse options

README.md

@@ -1,5 +1,7 @@
 # KIN and KINgaroo
 
+[![](https://anaconda.org/bioconda/kin/badges/downloads.svg)](https://anaconda.org/bioconda/kin)
+
 KIN is a Hidden-Markov-Model-based approach to identify identity-by-descent fragments and to estimate the degree of relatedness from ancient DNA data. KIN can accurately determine up to 3rd-degree relatives and differentiate between sibling and parent-child relationships with as little as 0.05x coverage.
 
 KINgaroo is a software to generate input files for KIN from bamfiles. Optionally, KINgaroo incorporates an adjustment for contamination and an additional model to estimate the location of long runs of homozygosity. This helps KIN to improve classification accuracy.

pypackage/kin/KIN/__main__.py

@@ -17,22 +17,22 @@ def cli():
     parser = argparse.ArgumentParser(description="Relatedness and IBD estimates")
 
     parser.add_argument('-I', '--input_location',
-                        type=str, metavar='',  required=True,
+                        type=str, required=True,
                         help='input files location')
     parser.add_argument('-O', '--output_location',
-                        type=str, metavar='', required=True,
+                        type=str, required=True,
                         help='Output files location')
     parser.add_argument('-r', '--ROH_file_location',
-                        type=str, metavar='',
+                        type=str,
                         help='ROH files location')
     parser.add_argument('-c', '--cores',
-                        type=int, metavar='',
+                        type=int,
                         help='Number of cores available')
     parser.add_argument('-t', '--threshold',
-                        type=int, metavar='',
+                        type=int,
                         help='Minimum number of sites in a window for ROH implementation')
     parser.add_argument('-p', '--diversity_parameter_p_0',
-                        type=float, metavar='',
+                        type=float, metavar='p_0',
                         help='Input p_0 parameter, if you do not want to calculate it from given samples (Keep it same as that for KINgaroo)')
 
     return parser.parse_args()

pypackage/kingaroo/KINgaroo/__main__.py

@@ -17,55 +17,55 @@ def cli():
     parser = argparse.ArgumentParser(description="Input generation pipeline for KIN")
 
     parser.add_argument('-bam', '--bamfiles_location',
-                        type=str, metavar='',  required=True,
+                        type=str, required=True,
                         help='bamfiles directory')
     parser.add_argument('-bed', '--bedfile',
-                        type=str, metavar='',  required=True,
+                        type=str, required=True,
                         help='path to bedfile')
     parser.add_argument('-T', '--target_location',
-                        type=str, metavar='', required=True,
+                        type=str, required=True,
                         help='file with bamfile names that should be used without extension')
     parser.add_argument('-cnt', '--contam_parameter',
-                        type=float, metavar='', required=True,
+                        type=float, required=True,
                         help='Enter 0 for no contamination correction. Enter 1 for contamination correction with divergence calculated from vcf.gz. Enter divergence (between 0 and 1) if known.')
     parser.add_argument('-c', '--cores',
-                        type=int, metavar='',
+                        type=int,
                         help='Number of cores available')
     parser.add_argument('-i', '--interval',
-                        type=int, metavar='',
+                        type=int,
                         help='Length of a genomic window in bases. Options:1000000, 10000000 (by default 10000000)')
     parser.add_argument('-t', '--threshold',
-                        type=int, metavar='',
+                        type=int,
                         help='p_0 is estimated with all libraries that have atleast t number of informative windows (by default t=10)')
     parser.add_argument('-cest', '--contamination_estimates',
-                        type=str, metavar='',
+                        type=str,
                         help='tab-separated contamination estimates file with columns: name,contamination')
     parser.add_argument('-d', '--divergence_file',
-                        type=str, metavar='',
+                        type=str,
                         help='indexed compressed vcf file with an individual from target and contaminating populations each. Diploid Genotypes (GT) should be represented')
     parser.add_argument('-tar', '--target_ind',
-                        type=str, metavar='',
+                        type=str,
                         help='Name of target individual in divergence_vcf file')
     parser.add_argument('-cont', '--contaminating_ind',
-                        type=str, metavar='',
+                        type=str,
                         help='Name of contaminating individual in divergence_vcf file')
     parser.add_argument('-r', '--roh',
-                        type=int, metavar='',
+                        type=int,
                         help='Enter 1 if you need ROH estimates. Enter 0 if you already have the positions of ROH tracts (by default:1).')
     parser.add_argument('-p', '--diversity_parameter_p_0',
-                        type=float, metavar='',
+                        type=float,
                         help='Enter p_0 estimate for input to ROH-HMM, if quality of samples is not good enough to estimate p_0.')
     parser.add_argument('-n', '--noisy_wins',
-                        type=str, metavar='',
+                        type=str,
                         help='You can optionally specify the noisy windows that should be filtered out in a file with list of window indexes (0-based).')
     parser.add_argument('-test', '--test_input',
-                        type=int, metavar='',
+                        type=int,
                         help='Enter 1 to test your input files')
     parser.add_argument('-N', '--number_of_chromosomes',
-                        type=int, metavar='',
+                        type=int,
                         help='Enter the total number of chromosomes. Default=22')
     parser.add_argument('-s', '--sort_index',
-                        type=int, metavar='',
+                        type=int,
                         help='Enter 1 if you need to sort and index the bamfiles. Enter 0 to skip this step (by default:1).')
     return parser.parse_args()