From e5cb4b1ab7034857622f440f759d073bfb8e0854 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 10 Oct 2007 07:39:30 +0000
Subject: [PATCH] Explicitly specify pairs of species to do projections.
Also specify host etc to use load_registry_from_db() in project_display_xrefs.pl so don't have to specify everything in conf file.
---
.../xref_projection/submit_projections.pl | 140 +++++++++++-------
1 file changed, 86 insertions(+), 54 deletions(-)
diff --git a/misc-scripts/xref_projection/submit_projections.pl b/misc-scripts/xref_projection/submit_projections.pl
index 0f4adecc48..67bf7ec047 100644
--- a/misc-scripts/xref_projection/submit_projections.pl
+++ b/misc-scripts/xref_projection/submit_projections.pl
@@ -8,7 +8,13 @@ my $release = 47;
my $base_dir = "/lustre/work1/ensembl/gp1/projections/";
-my $conf = "release_47.ini"; # registry config file
+my $conf = "release_47.ini"; # registry config file, specifies Compara location
+
+# location of other databases
+my $host = "ens-staging";
+my $port = 3306;
+my $user = "ensadmin";
+my $pass = "ensembl";
# -------------------------- end of config ----------------------------
@@ -26,35 +32,82 @@ if (! -e $dir) {
}
# common options
-my $opts = "-conf $conf -release $release -quiet";
-
-my ($o, $e, $n);
+my $opts = "-conf $conf -host $host -user $user -port $port -pass $pass -version $release -release $release -quiet -nobackup";
+
+my @names_1_1 = (["human", "chimp" ],
+ ["human", "opossum" ],
+ ["human", "dog" ],
+ ["human", "cow" ],
+ ["human", "macaque" ],
+ ["human", "chicken" ],
+ ["human", "xenopus" ],
+ ["human", "guinea_pig" ],
+ ["human", "armadillo" ],
+ ["human", "small_hedgehog" ],
+ ["human", "european_hedgehog"],
+ ["human", "cat" ],
+ ["human", "elephant" ],
+ ["human", "bat" ],
+ ["human", "platypus" ],
+ ["human", "rabbit" ],
+ ["human", "galago" ],
+ ["human", "european_shrew" ],
+ ["human", "squirrel" ],
+ ["human", "ground_shrew" ],
+ ["mouse", "rat" ]);
+
+my @names_1_many = (["human", "zebrafish" ],
+ ["human", "medaka" ],
+ ["human", "tetraodon" ],
+ ["human", "fugu" ],
+ ["human", "stickleback"]);
+
+
+my @go_terms = (["human", "mouse" ],
+ ["human", "rat" ],
+ ["human", "dog" ],
+ ["human", "chicken" ],
+ ["human", "cow" ],
+ ["human", "chimp" ],
+ ["human", "macaque" ],
+ ["human", "guinea_pig"],
+ ["drosophila", "anopheles" ],
+ ["drosophila", "aedes" ],
+ ["mouse", "human" ],
+ ["mouse", "rat" ],
+ ["mouse", "dog" ],
+ ["mouse", "chicken" ],
+ ["mouse", "cow" ],
+ ["rat", "human" ],
+ ["rat", "mouse" ],
+ ["danio", "xenopus" ],
+ ["danio", "fugu" ],
+ ["danio", "tetraodon" ],
+ ["xenopus", "danio" ]);
+
+my ($from, $to, $o, $e, $n);
# ----------------------------------------
# Display names
-# human to chimp,opossum,dog,cow,macaque,chicken,xenopus,pig,armadillo,small_hedgehog,european_hedgehog,cat,elephant,macaque,bat,platypus,rabbit,galago,european_shrew,squirrel,ground_shrew
-foreach my $to ("chimp", "opossum", "dog", "cow", "macaque", "chicken", "xenopus", "guinea_pig", "armadillo", "small_hedgehog", "european_hedgehog", "cat", "elephant", "bat", "platypus", "rabbit", "galago", "european_shrew", "squirrel", "ground_shrew") {
- $o = "$dir/names_human_$to.out";
- $e = "$dir/names_human_$to.err";
- $n = substr("n_hum_$to", 0, 10); # job name display limited to 10 chars
- system "bsub -o $o -e $e -J $n perl project_display_xrefs.pl $opts -from human -to $to -names -delete_names -no_database";
+# 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
+ print "Submitting name projection from $from to $to\n";
+ system "bsub -o $o -e $e -J $n perl project_display_xrefs.pl $opts -from $from -to $to -names -delete_names -no_database";
}
-# mouse to rat
-foreach my $to ("rat") { # don't need the loop but may add more species later
- $o = "$dir/names_mouse_$to.out";
- $e = "$dir/names_mouse_$to.err";
- $n = substr("n_mou_$to", 0, 10);
- system "bsub -o $o -e $e -J $n perl project_display_xrefs.pl $opts -from mouse -to $to -names -delete_names -no_database";
-}
-
-# human to fish - note use of -one_to_many option for 1-many projections
-foreach my $to ("zebrafish", "medaka", "tetraodon", "fugu", "stickleback") {
- $o = "$dir/names_human_$to.out";
- $e = "$dir/names_human_$to.err";
- $n = substr("n_hum_$to", 0, 10);
- system "bsub -o $o -e $e -J $n perl project_display_xrefs.pl $opts -from human -to $to -names -delete_names -no_database -one_to_many";
+# 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 -o $o -e $e -J $n perl project_display_xrefs.pl $opts -from from -to $to -names -delete_names -no_database -one_to_many";
}
# ----------------------------------------
@@ -62,37 +115,16 @@ foreach my $to ("zebrafish", "medaka", "tetraodon", "fugu", "stickleback") {
$opts .= " -nobackup";
-# human to mouse, rat, dog, chicken, cow, chimp, macaque, guinea_pig
-foreach my $to ("mouse", "rat", "dog", "chicken", "cow", "chimp", "macaque", "guinea_pig") {
- $o = "$dir/go_human_$to.out";
- $e = "$dir/go_human_$to.err";
- $n = substr("g_hum_$to", 0, 10);
- system "bsub -o $o -e $e -J $n perl project_display_xrefs.pl $opts -from human -to $to -go_terms -delete_go_terms";
-}
-
-# drosophila to anopheles, aedes
-foreach my $to ("anopheles", "aedes") {
- $o = "$dir/go_drosophila_$to.out";
- $e = "$dir/go_drosophila_$to.err";
- $n = substr("g_dros_$to", 0, 10);
- system "bsub -o $o -e $e -J $n perl project_display_xrefs.pl $opts -from drosophila -to $to -go_terms -delete_go_terms";
+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 -o $o -e $e -J $n perl project_display_xrefs.pl $opts -from $from -to $to -go_terms -delete_go_terms";
}
# ----------------------------------------
-# GO terms - mouse to human, rat, dog, chicken, cow
-# Have to use job dependencies since these jobs need to run after the corresponding human-X projections have
-# Note need to not use -delete the second time around
-foreach my $to ("human", "rat", "dog", "chicken", "cow") {
- $o = "$dir/go_mouse_$to.out";
- $e = "$dir/go_mouse_$to.err";
- $n = substr("g_mou_$to", 0, 10);
- my $d;
- if ($to eq 'human') { # no "human-human" to depend upon
- $d = '';
- } else {
- my $depend_job_name = substr("g_hum_$to", 0, 10);
- $d = "-w 'ended($depend_job_name)'";
- }
- system "bsub -o $o -e $e -J $n $d perl project_display_xrefs.pl $opts -from mouse -to $to -go_terms";
-}
+
+
--
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