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Commit 163e43ea authored by Kieron Taylor's avatar Kieron Taylor :angry:
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Altered to remove ugly paired lists of species. 

Execution order now defined in an array, and species pairs now defined through a hash.
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misc-scripts/xref_projection/submit_projections.pl
+ 211
− 185
View file @ 163e43ea
......@@ -61,195 +61,217 @@ my $script_opts = "-conf '$conf' -registryconf '$registryconf' -version '$releas
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);
my %names_1_1;
$names_1_1{'human'} = [qw(
alpaca
anolis
armadillo
bushbaby
cat
chicken
chimp
coelacanth
cow
dolphin
elephant
gibbon
gorilla
ground_shrew
guinea_pig
horse
hyrax
macaque
marmoset
megabat
microbat
mouse_lemur
opossum
orang_utan
panda
pig
pika
platypus
sloth
squirrel
rabbit
tarsier
tasmanian_devil
tenrec
tree_shrew
turkey
wallaby
western_european_hedgehog
xenopus
zebrafinch
)];
$names_1_1{'mouse'} = [qw(
kangaroo_rat
rat
)];
my %names_1_many;
$names_1_many{'human'} = [qw(
cod
fugu
lamprey
medaka
stickleback
tetraodon
tilapia
zebrafish
)];
my %go_terms;
$go_terms{'human'} = [qw(
alpaca
anolis
armadillo
bushbaby
cat
chicken
chimp
coelacanth
cow
dog
dolphin
elephant
gibbon
gorilla
ground_shrew
guinea_pig
horse
hyrax
kangaroo_rat
macaque
marmoset
megabat
microbat
mouse
mouse_lemur
opossum
orang_utan
panda
pig
platypus
sloth
squirrel
stickleback
pika
rabbit
rat
tarsier
tasmanian_devil
tenrec
tree_shrew
turkey
wallaby
western_european_hedgehog
zebrafinch
)];
$go_terms{'mouse'} = [qw(
alpaca
anolis
armadillo
bushbaby
cat
chicken
chimp
cow
dog
dolphin
elephant
gorilla
ground_shrew
guinea_pig
horse
hyrax
human
kangaroo_rat
macaque
marmoset
megabat
microbat
mouse_lemur
opossum
orang_utan
panda
pig
pika
platypus
rabbit
rat
sloth
squirrel
stickleback
tarsier
tasmanian_devil
tenrec
tree_shrew
turkey
wallaby
western_european_hedgehog
zebrafinch
)];
$go_terms{'rat'} = [qw(
human
mouse
)];
$go_terms{'zebrafish'} = [qw(
cod
coelacanth
fugu
lamprey
stickleback
tetraodon
tilapia
xenopus
)];
$go_terms{'xenopus'} = [qw(zebrafish)];
my @execution_order = ( 'human', 'mouse', 'rat', 'zebrafish');
# ----------------------------------------
# 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";
foreach my $species (keys %names_1_1) {
foreach my $to (@{$species}) {
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";
foreach my $from (@execution_order) {
if (not exists($names_1_1{$from})) {next;}
foreach my $to (@{$names_1_1{$from}}) {
my $o = "$dir/names_${from}_$to.out";
my $e = "$dir/names_${from}_$to.err";
my $n = substr("n_${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";
foreach my $from (keys %names_1_many) {
foreach my $to (@{$names_1_many{$from}}) {
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";
foreach my $from (@execution_order) {
if (not exists($names_1_many{$from})) {next;}
foreach my $to (@{$names_1_many{$from}}) {
my $o = "$dir/names_${from}_$to.out";
my $e = "$dir/names_${from}_$to.err";
my $n = substr("n_${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";
}
}
# ----------------------------------------
......@@ -258,22 +280,26 @@ foreach my $pair (@names_1_many) {
$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 $from (keys %go_terms) {
foreach my $to (@{$go_terms{$from}}) {
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";
foreach my $from (@execution_order) {
if (not exists($go_terms{$from})) {next;}
foreach my $to (@{$go_terms{$from}}) {
my $o = "$dir/go_${from}_$to.out";
my $e = "$dir/go_${from}_$to.err";
my $n = substr("g_${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";
}
}
# ----------------------------------------
......
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