use strict;
use Data::Dumper;
use Bio::EnsEMBL::ApiVersion qw/software_version/;
$Data::Dumper::Useqq=1;
$Data::Dumper::Terse = 1;
$Data::Dumper::Indent = 0;
# Submits the display name and GO term projections as farm jobs
# Remember to check/set the various config optons
# ------------------------------ config -------------------------------
my $release = software_version();
my $base_dir = "mypath";
my $conf = "release_${release}.ini"; # registry config file, specifies Compara location
# location of other databases
my @config = ( {
'-host' => 'HOST',
'-port' => 'PORT',
'-user' => 'USER',
'-pass' => 'PASS',
'-db_version' => $release
},
{
'-host' => 'HOST',
'-port' => 'PORT',
'-user' => 'USER',
'-pass' => 'PASS',
'-db_version' => $release
} );
my $registryconf = Dumper(\@config);
# load limit for ens-staging MySQL instance above which jobs won't be started
my $limit = 200;
# -------------------------- end of config ----------------------------
# check that base directory exists
die ("Cannot find base directory $base_dir") if (! -e $base_dir);
# create release subdir if necessary
my $dir = $base_dir. $release;
if (! -e $dir) {
mkdir $dir;
print "Created $dir\n";
} else {
print "Cleaning and re-using $dir\n";
unlink <$dir/*.out>, <$dir/*.err>;
}
# common options
my $script_opts = "-conf '$conf' -registryconf '$registryconf' -version '$release' -release '$release' -quiet";
my $bsub_opts = "";
$bsub_opts .= "-M2000000 -R'select[mem>2000] rusage[mem=2000]'";
my @names_1_1 = (["human", "chimp" ],
["human", "opossum" ],
["human", "dog" ],
["human", "cow" ],
["human", "macaque" ],
["human", "chicken" ],
["human", "xenopus" ],
["human", "guinea_pig" ],
["human", "pig" ],
["human", "marmoset" ],
["human", "armadillo" ],
["human", "tenrec" ],
["human", "western_european_hedgehog"],
["human", "cat" ],
["human", "elephant" ],
["human", "microbat" ],
["human", "platypus" ],
["human", "rabbit" ],
["human", "bushbaby" ],
["human", "ground_shrew" ],
["human", "squirrel" ],
["human", "tree_shrew" ],
["human", "pika" ],
["human", "mouse_lemur" ],
["human", "wallaby" ],
["human", "horse" ],
["human", "orang_utan" ],
["human", "gibbon" ],
["human", "dolphin" ],
["human", "hyrax" ],
["human", "megabat" ],
["human", "tarsier" ],
["human", "alpaca" ],
["human", "gorilla" ],
["human", "anolis" ],
["human", "sloth" ],
["human", "zebrafinch" ],
["human", "panda" ],
["human", "turkey" ],
["human", "tasmanian_devil" ],
["human", "coelacanth" ],
["mouse", "kangaroo_rat" ],
["mouse", "rat" ]);
my @names_1_many = (["human", "zebrafish" ],
["human", "medaka" ],
["human", "tetraodon" ],
["human", "fugu" ],
["human", "lamprey" ],
["human", "cod" ],
["human", "tilapia" ],
["human", "stickleback"]);
my @go_terms = (["human", "mouse" ],
["human", "rat" ],
["human", "dog" ],
["human", "chicken" ],
["human", "cow" ],
["human", "chimp" ],
["human", "macaque" ],
["human", "guinea_pig" ],
["human", "pig" ],
["human", "marmoset" ],
["human", "bushbaby" ],
["human", "rabbit" ],
["human", "cat" ],
["human", "ground_shrew" ],
["human", "western_european_hedgehog"],
["human", "microbat" ],
["human", "armadillo" ],
["human", "elephant" ],
["human", "tenrec" ],
["human", "opossum" ],
["human", "platypus" ],
["human", "squirrel" ],
["human", "tree_shrew" ],
["human", "pika" ],
["human", "mouse_lemur" ],
["human", "wallaby" ],
["human", "horse" ],
["human", "orang_utan" ],
["human", "gibbon" ],
["human", "dolphin" ],
["human", "hyrax" ],
["human", "megabat" ],
["human", "tarsier" ],
["human", "alpaca" ],
["human", "kangaroo_rat" ],
["human", "gorilla" ],
["human", "sloth" ],
["human", "zebrafinch" ],
["human", "anolis" ],
["human", "panda" ],
["human", "turkey" ],
["human", "tasmanian_devil"],
["human", "coelacanth" ],
["mouse", "human" ],
["mouse", "rat" ],
["mouse", "dog" ],
["mouse", "chicken" ],
["mouse", "cow" ],
["mouse", "chimp" ],
["mouse", "macaque" ],
["mouse", "guinea_pig" ],
["mouse", "pig" ],
["mouse", "marmoset" ],
["mouse", "bushbaby" ],
["mouse", "rabbit" ],
["mouse", "cat" ],
["mouse", "ground_shrew" ],
["mouse", "western_european_hedgehog"],
["mouse", "microbat" ],
["mouse", "armadillo" ],
["mouse", "elephant" ],
["mouse", "tenrec" ],
["mouse", "opossum" ],
["mouse", "platypus" ],
["mouse", "squirrel" ],
["mouse", "tree_shrew" ],
["mouse", "pika" ],
["mouse", "horse" ],
["mouse", "orang_utan" ],
["mouse", "mouse_lemur" ],
["mouse", "wallaby" ],
["mouse", "dolphin" ],
["mouse", "hyrax" ],
["mouse", "megabat" ],
["mouse", "tarsier" ],
["mouse", "alpaca" ],
["mouse", "kangaroo_rat" ],
["mouse", "gorilla" ],
["mouse", "sloth" ],
["mouse", "zebrafinch" ],
["mouse", "anolis" ],
["mouse", "panda" ],
["mouse", "tasmanian_devil"],
["rat", "human" ],
["rat", "mouse" ],
["zebrafish", "xenopus" ],
["zebrafish", "fugu" ],
["zebrafish", "tetraodon" ],
["zebrafish", "stickleback"],
["zebrafish", "lamprey" ],
["zebrafish", "cod" ],
["zebrafish", "coelacanth" ],
["zebrafish", "tilapia" ],
["human", "stickleback" ],
["mouse", "stickleback" ],
["mouse", "turkey" ],
["xenopus", "danio" ]);
my ($from, $to, $o, $e, $n);
# ----------------------------------------
# Display names
print "Deleting projected names (one to one)\n";
foreach my $pair (@names_1_1) {
($from, $to) = @$pair;
system "perl project_display_xrefs.pl $script_opts -to $to -delete_names -delete_only";
}
# 1:1
foreach my $pair (@names_1_1) {
($from, $to) = @$pair;
$o = "$dir/names_${from}_$to.out";
$e = "$dir/names_${from}_$to.err";
$n = substr("n_${from}_$to", 0, 10); # job name display limited to 10 chars
my $all = ($from eq "human") ? "" : "--all_sources"; # non-human from species -> use all sources
print "Submitting name projection from $from to $to\n";
system "bsub $bsub_opts -o $o -e $e -J $n perl project_display_xrefs.pl $script_opts -from $from -to $to -names -no_database $all";
}
print "Deleting projected names (one to many)\n";
foreach my $pair (@names_1_many) {
($from, $to) = @$pair;
system "perl project_display_xrefs.pl $script_opts -to $to -delete_names -delete_only";
}
# 1:many
foreach my $pair (@names_1_many) {
($from, $to) = @$pair;
$o = "$dir/names_${from}_$to.out";
$e = "$dir/names_${from}_$to.err";
$n = substr("n_${from}_$to", 0, 10);
print "Submitting name projection from $from to $to (1:many)\n";
system "bsub $bsub_opts -o $o -e $e -J $n perl project_display_xrefs.pl $script_opts -from $from -to $to -names -no_database -one_to_many";
}
# ----------------------------------------
# GO terms
$script_opts .= " -nobackup";
print "Deleting projected GO terms\n";
foreach my $pair (@go_terms) {
($from, $to) = @$pair;
system "perl project_display_xrefs.pl $script_opts -to $to -delete_go_terms -delete_only";
}
foreach my $pair (@go_terms) {
($from, $to) = @$pair;
$o = "$dir/go_${from}_$to.out";
$e = "$dir/go_${from}_$to.err";
$n = substr("g_${from}_$to", 0, 10);
print "Submitting GO term projection from $from to $to\n";
system "bsub $bsub_opts -q long -o $o -e $e -J $n perl project_display_xrefs.pl $script_opts -from $from -to $to -go_terms";
}
# ----------------------------------------