from datetime import datetime
import ftplib
import os
import sys
from distutils import spawn
try:
import pypez
import pysam
import pandas # make sure all dependencies are installed
except ImportError as e:
sys.exit("ERROR: Python module not installed. %s. Please run 'pip install -r requirements.txt' " % e)
for executable in ['wget', 'Rscript', 'tabix', 'vt']:
assert spawn.find_executable(executable), "Command %s not found, see README" % executable
p = configargparse.getArgParser()
g = p.add_argument_group('main args')
g.add("--b37-genome", help="b37 .fa genome reference file", required=True)
g.add("--b38-genome", help="b38 .fa genome reference file. NOTE: chromosome names must be like '1', '2'.. 'X', 'Y', 'MT'.", required=True)
g.add("-X", "--clinvar-xml", help="The local filename of the ClinVarFullRelase.xml.gz file. If not set, grab the latest from NCBI.")
g.add("-S", "--clinvar-variant-summary-table", help="The local filename of the variant_summary.txt.gz file. If not set, grab the latest from NCBI.")
g.add("-E", "--exac-sites-vcf", help="ExAC sites vcf file. If specified, a clinvar table with extra ExAC fields will also be created.")
g.add("-GE", "--gnomad-exome-sites-vcf", help="gnomAD exome sites vcf file. If specified, a clinvar table with extra gnomAD exome info fields will also be created.")
g.add("-GG", "--gnomad-genome-sites-vcf", help="gnomAD genome sites vcf file. If specified, a clinvar table with extra gnomAD genome info fields will also be created.")
g = p.add_mutually_exclusive_group()
g.add("--single-only", dest="single_or_multi", action="store_const", const="single", help="Only generate the single-variant tables")
g.add("--multi-only", dest="single_or_multi", action="store_const", const="multi", help="Only generate the multi-variant tables")
pypez.init_command_line_args()
args = p.parse_args()
for key, value in args.__dict__.items():
import ftplib
import os
import sys
from distutils import spawn
try:
import configargparse
import pypez
import pysam
import pandas # make sure all dependencies are installed
except ImportError as e:
sys.exit("ERROR: Python module not installed. %s. Please run 'pip install -r requirements.txt' " % e)
for executable in ['wget', 'tabix', 'vt']:
assert spawn.find_executable(executable), "Command %s not found, see README" % executable
p = configargparse.getArgParser()
g = p.add_argument_group('main args')
g.add("--b37-genome", help="b37 .fa genome reference file", default=None, required=False)
g.add("--b38-genome", help="b38 .fa genome reference file. NOTE: chromosome names must be like '1', '2'.. 'X', 'Y', 'MT'.", default=None, required=False)
g.add("-X", "--clinvar-xml", help="The local filename of the ClinVarFullRelase.xml.gz file. If not set, grab the latest from NCBI.")
g.add("-S", "--clinvar-variant-summary-table", help="The local filename of the variant_summary.txt.gz file. If not set, grab the latest from NCBI.")
g.add("-E", "--exac-sites-vcf", help="ExAC sites vcf file. If specified, a clinvar table with extra ExAC fields will also be created.")
g.add("-GE", "--gnomad-exome-sites-vcf", help="gnomAD exome sites vcf file. If specified, a clinvar table with extra gnomAD exome info fields will also be created.")
g.add("-GG", "--gnomad-genome-sites-vcf", help="gnomAD genome sites vcf file. If specified, a clinvar table with extra gnomAD genome info fields will also be created.")
g.add("--output-prefix", default="../output/", help="Final output files will have this prefix")
g.add("--tmp-dir", default="./output_tmp", help="Temporary output files will have this prefix")
g = p.add_mutually_exclusive_group()
g.add("--single-only", dest="single_or_multi", action="store_const", const="single", help="Only generate the single-variant tables")
g.add("--multi-only", dest="single_or_multi", action="store_const", const="multi", help="Only generate the multi-variant tables")
