Commit e8d3edc6 authored by peguerin's avatar peguerin
Browse files

version argument

parent a7a3d3e4
......@@ -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')
......
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