version argument

mkbdr/arguments.py

@@ -3,6 +3,9 @@ import sys
 import os
 import pandas
 
+from mkbdr import __version__
+
+
 HELPER_TEXT ="""
 .___  ___.  __  ___ .______    _______  .______      
 |   \/   | |  |/  / |   _  \  |       \ |   _  \     
@@ -16,12 +19,12 @@ _______________________________________________________________________________
 
 Pierre-Edouard GUERIN, Laetitia MATHON, Virginie MARQUES, Stephanie MANEL
 CNRS, EPHE, Sorbonne University, Montpellier, France
-version 1.1 "Peau de Lezard" March 2021
+version {0} March 2021
 Usage:
 > mkbdr [options]
 For help:
 > mkbdr --help
-"""
+""".format(__version__)
 
 
 def check_taxdumpdir(ncbiTaxdumpDir):
@@ -60,6 +63,7 @@ def check_curatecsv(curateCsvFile):
 
 def parse_args(usage=HELPER_TEXT):
     parser = argparse.ArgumentParser(description='mkbdr - to build a custom metabarcoding reference database.')
+    parser.add_argument("-v","--version", action="version", help="Show version number and exit", version=__version__)
 
     subprasers = parser.add_subparsers(dest='command')
 
@@ -70,14 +74,13 @@ def parse_args(usage=HELPER_TEXT):
     validate.add_argument("-e","--ncbi_taxonomy_edition", type=str, default='NA', help='Folder of NCBI taxonomy files to edit in order to add new taxonomy nodes')
     validate.add_argument("-o","--output_prefix", type=str, help='prefix of the output FASTA such as [PREFIX].fasta')
 
-
-    curegen = subprasers.add_parser('curegen', help='try to correct wrong taxonomy')
+    curegen = subprasers.add_parser('curegen', help='generate curation file to correct wrong taxonomy')
     curegen.add_argument("-f","--fasta", type=str, help='path of the barcodes sequences FASTA file', required=True)
     curegen.add_argument("-d","--database_globalnames", type=str, help="Name of the selected database from GlobalNames i.e. 'Catalogue of Life' or 'Fishbase Cache'", required=False, default='FishBase Cache')
     curegen.add_argument("-o","--output_prefix", type=str, help='prefix of the output curated taxonomy CSV such as [PREFIX].csv')
     curegen.add_argument("-l","--ncbi_taxdump_load",  type=str, default='NA', help='load NCBI taxonomy archive')
 
-    init_ncbi_taxdump = subprasers.add_parser('init_ncbi_taxdump', help='Download and decompress the NCBI taxdump archive')
+    init_ncbi_taxdump = subprasers.add_parser('init_ncbi_taxdump', help='download the NCBI taxdump archive')
     init_ncbi_taxdump.add_argument("-f", "--folder_path", type=str, help='Folder path where to download the NCBI taxdump archive', required=False, default='.')
     init_ncbi_taxdump.add_argument("-d", "--decompress", action='store_true', help='Decompress the archive')