vep

#!/usr/bin/env perl
# Copyright [2016-2023] EMBL-European Bioinformatics Institute
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

use Getopt::Long;
use FindBin qw($RealBin);
use lib $RealBin;
use lib $RealBin.'/modules';
use Bio::EnsEMBL::VEP::Runner;
use Bio::EnsEMBL::VEP::Utils qw(get_version_string);

my $arg_count = scalar @ARGV;

my $config = {};
my @vep_params = @{Bio::EnsEMBL::VEP::Config::VEP_PARAMS};
GetOptions($config, @vep_params) or die "ERROR: Failed to parse command-line flags\n";

&usage && exit(0) if (!$arg_count) || $config->{help};
die("ERROR: Unexpected extra command-line parameter(s): " . join(", ", @ARGV)) if scalar @ARGV;

warn("WARNING: More than one output file command-line flag provided. Using the last value provided: '@{$config->{output_file}}[-1]' \n") unless (scalar @{$config->{output_file}} <= 1);
$config->{output_file}=@{$config->{output_file}}[-1] if ($config->{output_file});

$config->{database} ||= 0;

my $runner = Bio::EnsEMBL::VEP::Runner->new($config);

if($config->{show_cache_info}) {
  my $info = $runner->get_output_header_info->{version_data};
  print "$_\t$info->{$_}\n" for keys %$info;
  exit(0);
}


$runner->run();



# outputs usage message
sub usage {

  my $versions = get_version_string($RealBin.'/.version');

  my $usage =<<END;
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

Versions:
  $versions

Help: dev\@ensembl.org , helpdesk\@ensembl.org
Twitter: \@ensembl

http://www.ensembl.org/info/docs/tools/vep/script/index.html

Usage:
./vep [--cache|--offline|--database] [arguments]

Basic options
=============

--help                 Display this message and quit

-i | --input_file      Input file
-o | --output_file     Output file
--force_overwrite      Force overwriting of output file
--species [species]    Species to use [default: "human"]

--everything           Shortcut switch to turn on commonly used options. See web
                       documentation for details [default: off]
--fork [num_forks]     Use forking to improve script runtime

For full option documentation see:
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html

END

  print $usage;
}


1;