no longer needed

misc-scripts/density_feature/glovar_snp_wrapper.pl

-#!/usr/local/bin/perl
-
-=head1 NAME
-
-glovar_snp_wrapper.pl -
-Wrapper for glovar_snp_density.pl
-
-=head1 SYNOPSIS
-
-    ./glovar_snp_density.pl
-        --species=Homo_sapiens
-        [--dry_run|-n]
-        [--avdump|-a]
-
-=head1 DESCRIPTION
-
-Wrapper for glovar_snp_density.pl to run it chromosome by chromosome. This is
-an attempt to avoid high memory footprints caused by a memory leak somerwhere
-in the API. See glovar_snp_density.pl for more detailed documentation.
-
-=head1 LICENCE
-
-This code is distributed under an Apache style licence:
-Please see http://www.ensembl.org/code_licence.html for details
-
-=head1 AUTHOR
-
-Patrick Meidl <pm2@sanger.ac.uk>
-
-=head1 CONTACT
-
-Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
-
-=cut
-
-use strict;
-BEGIN {
-    $ENV{'ENSEMBL_SERVERROOT'} = "../../..";
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/conf");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl-compara/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl-draw/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl-external/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl-otter/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/bioperl-live");
-}
-
-use SiteDefs;
-use EnsWeb;
-use Getopt::Long;
-
-my ($species, $dry, $avdump);
-&GetOptions(
-    "species=s" => \$species,
-    "dry_run"   => \$dry,
-    "n"         => \$dry,
-    "avdump"    => \$avdump,
-    "a"         => \$avdump,
-);
-
-unless ($species) {
-    print qq(Usage:
-    ./glovar_snp_density.pl
-        --species=Homo_sapiens
-        [--avdump|-a]
-        [--dry_run|-n]\n\n);
-    exit;
-}
-
-$ENV{'ENSEMBL_SPECIES'} = $species;
-
-## run glovar_snp_density.pl for each chromsome in this species
-my $command = "./glovar_snp_density.pl --species=$species";
-$command .= " -n" if ($dry);
-$command .= " -a" if ($avdump);
-foreach my $chr (@{$EnsWeb::species_defs->ENSEMBL_CHROMOSOMES}) {
-    warn "$command --chr=$chr\n";
-    system("$command --chr=$chr") == 0 or die "$command --chr=$chr failed: $!\n";
-}
-