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# The script lists databases/species which should have density features updated at the specified stage in the release cycle. There's an option for submitting a selected script.
use strict;
use Getopt::Long;
use DBI qw( :sql_types );
use Switch;
my $getdbs;
my $submit_script;
my $outdir;
my @host;
my @user;
my @pass;
my @port;
GetOptions( "getdbs|g", \$getdbs,
"submit|s=s", \$submit_script,
"outdir|o=s", \$outdir,
"host|h=s",\@host,
"user|u=s",\@user,
"pass|p=s",\@pass,
"port=s",\@port,
"help" , \&usage
);
my $host_count = @host;
my $user_count = @user;
my $pass_count = @pass;
usage() if (!defined @host || !defined @user || !defined @pass || $user_count != $host_count || $pass_count != $host_count);
my $port_count = @port;
my $host_string = join("\|",@host);
if ( (!defined @port) || ($port_count < $host_count) ) {
for (my $i=0; $i<$host_count;$i++) {
if (!defined $port[$i]) {
push(@port,3306);
}
}
}
# production/master database location:
my ( $mhost, $mport ) = ( 'ens-staging1', '3306' );
my ( $muser, $mpass ) = ( 'ensro', undef );
my $mdbname = 'ensembl_production';
#connect to the production database
my $prod_dsn = sprintf( 'DBI:mysql:host=%s;port=%d;database=%s',
$mhost, $mport, $mdbname );
my $prod_dbh = DBI->connect( $prod_dsn, $muser, $mpass,
{ 'PrintError' => 1, 'RaiseError' => 1 } );
#get the current release number
my ($current_release ) = $prod_dbh->selectrow_array('select max(db_release) from db where is_current = 1');
my @hosts = qw(ens-staging1, ens-staging2);
if (!$outdir) {
$outdir = $ENV{'PWD'};
} else {
#strip the final /
$outdir =~ s/\/$//;
#test if the directory exists
if (!-d $outdir) {
die("Directory $outdir does not exist.");
}
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}
if ( !defined $submit_script ) {
$getdbs = 1;
}
if ( defined $getdbs ) {
# ask the user which stage of the release cycle we're in
print <<CYCLE;
Where in the release cycle are we (0,1,2,3)?
0 - None of the below - exit program
1 - Genebuild and genebuild xrefs complete (excluding projected xrefs), all gene healthchecks cleared
2 - Compara homologies handed over and core xref projections complete
3 - Variation dbs handed over
CYCLE
my $response = <>;
if ( !defined $response or $response !~ /[0-4]/ ) {
print <<CYCLE2;
Please specify a valid option: 0, 1, 2 or 3:
Where in the release cycle are we (0,1,2,3)?
0 - None of the below - exit program
1 - Genebuild and genebuild xrefs complete (excluding projected xrefs), all gene healthchecks cleared
2 - Compara homologies handed over and core xref projections complete
3 - Variation dbs hand
CYCLE2
$response = <>;
}
if ($response == 0) {
exit(0);
}
#dbs for new species or changed assembly
my @new_sp_assem;
#dbs with changed gene sequence
my @chg_seq;
#dbs with changed repeats
my @chg_repeats;
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#dbs with new variation positions
my @chg_variation;
if ($response >= 1) {
#get new dbs, or changed assembly
@new_sp_assem = map { $_->[0] } @{ $prod_dbh->selectall_arrayref("select distinct concat(full_db_name,'|',db_host) from db_list dl join db d using (db_id) where is_current = 1 and db_type = 'core' and species_id not in (select distinct species_id from db where is_current <> 1 and db_type = 'core') union
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select distinct concat(full_db_name,'|',db_host) from db_list dl join db d using (db_id) where db_type = 'core' and is_current = 1 and species_id in (select distinct species_id from changelog_species cs join changelog c using (changelog_id) where release_id = $current_release and status not in ('cancelled','postponed') and assembly = 'Y')") };
#get dbs with changed sequence
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@chg_seq = map { $_->[0] } @{ $prod_dbh->selectall_arrayref("select distinct concat(full_db_name,'|',db_host) from db_list dl join db d using (db_id) where db_type = 'core' and is_current = 1 and species_id in (select distinct species_id from changelog_species cs join changelog c using (changelog_id) where release_id = $current_release and status not in ('cancelled','postponed') and gene_set = 'Y')") };
#get dbs with changed repeats
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@chg_repeats = map { $_->[0] } @{ $prod_dbh->selectall_arrayref("select distinct concat(full_db_name,'|',db_host) from db_list dl join db d using (db_id) where db_type = 'core' and is_current = 1 and species_id in (select distinct species_id from changelog_species cs join changelog c using (changelog_id) where release_id = $current_release and status not in ('cancelled','postponed') and repeat_masking = 'Y')") };
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print "1. Density features scripts which can be run when qenebuild and genebuild xrefs (excluding projected xrefs) are complete and all gene healthchecks are cleared: \n\n";
print "gene_gc.pl - run on all core databases (use the commands below or script submit_density_features.pl -submit gene_gc):\n";
for (my $i=0; $i<$host_count;$i++) {
print "\nbsub -q normal -J genegc_stats -oo ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_genegc.out -eo ".$outdir. "/core_dbs_".$current_release."_".$host[$i]."_genegc.err perl ../gene_gc.pl -h ".$host[$i]." -port ".$port[$i]." -u ".$user[$i]." -p ".$pass[$i]." -pattern 'core_".$current_release."'\n";
}
print "\npercent_gc_calc.pl – run on core databases for new species, or where sequence or assembly have changed (db names will be stored in file ./percent_gc_data.txt, to submit run submit_density_features.pl -submit percent_gc): \n";
my %array_union = ();
foreach my $element (@new_sp_assem, @chg_seq) { $array_union{$element}++ }
my @dbnames_hosts = sort(keys %array_union);
my $file_path = "./percent_gc_data.txt";
open(DATAFILE, ">$file_path") or die("Failed to open file $file_path for writing\n");
foreach my $dbname_host (@dbnames_hosts) {
my ($db_name, $host) = split(/\|/,$dbname_host);
if ( ($db_name =~ /core_/) && ( $host_string =~ /$host/) ) {
print DATAFILE $db_name."\t".$host."\n";
print $db_name."\t".$host."\n";
}
}
close DATAFILE;
print "\n\nrepeat_coverage_calc.pl – run on core databases for new species, or where sequence, assembly or repeats have changed (db names will be stored in file ./repeat_coverage_data.txt, to submit run submit_density_features.pl -submit repeat_coverage): \n";
foreach my $element (@chg_repeats) { $array_union{$element}++ }
@dbnames_hosts = sort(keys %array_union);
my $file_path = "./repeat_coverage_data.txt";
open(DATAFILE, ">$file_path") or die("Failed to open file $file_path for writing\n");
foreach my $dbname_host (@dbnames_hosts) {
my ($db_name, $host) = split(/\|/,$dbname_host);
if ( ($db_name =~ /core_/) && ( $host_string =~ /$host/) ) {
print DATAFILE $db_name."\t".$host."\n";
print $db_name."\t".$host."\n";
}
}
close DATAFILE;
}
if ($response >= 2) {
print "\n\n2. Density features scripts which can be run when Compara homologies are handed over and core xref projections are complete:\n\n";
print "gene_density_calc.pl - run on all core dbs (use the commands below or script submit_density_features.pl -submit gene_density)\n";
for (my $i=0; $i<$host_count;$i++) {
print "\nbsub -q normal -J gene_density -oo ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_gene.out -eo ".$outdir. "/core_dbs_".$current_release."_".$host[$i]."_gene.err perl ./gene_density_calc.pl -h ".$host[$i]." -port ".$port[$i]." -u ".$user[$i]." -p ".$pass[$i]." -pattern 'core_".$current_release."'\n";
}
print "\n\nseq_region_stats.pl (gene stats option only) - run on all core databases (use the commands below or script submit_density_features.pl -submit seq_region_stats_gene)\n";
for (my $i=0; $i<$host_count;$i++) {
print "\nbsub -q normal -J seqreg_stats_gene -oo ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_seqreg_gene.out -eo ".$outdir. "/core_dbs_".$current_release."_".$host[$i]."_seqreg_gene.err perl ./seq_region_stats.pl -h ".$host[$i]." -port ".$port[$i]." -u ".$user[$i]." -p ".$pass[$i]." -pattern 'core_".$current_release."' -s gene\n";
}
}
if ($response == 3) {
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print "\n\n3. Density features scripts which can be run when Variation dbs are handed over:\n";
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print "\nvariation_density.pl - run for new species or where the core assembly has changed, or if there are any changes to variation positions in the variation database (species will be stored in file ./variation_density_data.txt, to submit run submit_density_features.pl -submit variation_density):\n";
#get species for new dbs or changed assembly or where variation positions have changed
@chg_variation = map { $_->[0] } @{ $prod_dbh->selectall_arrayref("select distinct concat(full_db_name,'|',db_host) from db_list dl join db d using (db_id) where db_type = 'core' and is_current = 1 and species_id in (select distinct species_id from changelog_species cs join changelog c using (changelog_id) where release_id = $current_release and status not in ('cancelled','postponed') and variation_pos_changed = 'Y')") };
my %array_union = ();
foreach my $element (@new_sp_assem, @chg_variation) { $array_union{$element}++ }
my @dbnames_hosts = sort(keys %array_union);
my $file_path = "./variation_density_data.txt";
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open(DATAFILE, ">$file_path") or die("Failed to open file $file_path for writing\n");
foreach my $dbname_host (@dbnames_hosts) {
my ($db_name, $host) = split(/\|/,$dbname_host);
if ( ($db_name =~ /([^\s]+)_core/) && ( $host_string =~ /$host/) ) {
$db_name =~ /([^\s]+)_core/;
print DATAFILE $1 ."\t".$host."\n";
print $1 ."\t".$host."\n";
}
}
close DATAFILE;
print "\n\nseq_region_stats.pl (snp stats option only) - run on core databases for new species or if the assembly changed, or if the variation positions have changed in the corresponding variation db (db names will be stored in file ./seq_region_stats_snp_data.txt, to submit run submit_density_features.pl -submit seq_region_stats_snp):\n";
my $file_path = "./seq_region_stats_snp_data.txt";
open(DATAFILE, ">$file_path") or die("Failed to open file $file_path for writing\n");
foreach my $dbname_host (@dbnames_hosts) {
my ($db_name, $host) = split(/\|/,$dbname_host);
if ( ($db_name =~ /core_/) && ( $host_string =~ /$host/) ) {
print DATAFILE $db_name."\t".$host."\n";
print $db_name."\t".$host."\n";
}
}
close DATAFILE;
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}
} else {
#submit selected script
my @cmd;
my $data_file;
my @print_message;
my $error;
my %error_message;
my $queue;
my $file_name_end;
my $script;
my $script_title;
my $job_name;
my $option;
switch ($submit_script) {
case 'gene_gc' {
for (my $i=0; $i<$host_count;$i++) {
push(@cmd, "bsub -q normal -J genegc_stats -oo ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_genegc.out -eo ".$outdir. "/core_dbs_".$current_release."_".$host[$i]."_genegc.err perl ../gene_gc.pl -h ".$host[$i]." -port ".$port[$i]." -u ".$user[$i]." -p ".$pass[$i]." -pattern 'core_".$current_release."'");
push(@print_message,"Submitting gene GC calculation for host ".$host[$i]." to queue 'normal'. The output from this job goes to the file ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_genegc.out\n");
}
}
case 'percent_gc' {
$data_file = "percent_gc_data.txt";
$queue = "normal";
$job_name = "gc_calc";
$file_name_end = "_gc";
$script = "percent_gc_calc.pl";
$script_title = "percent GC calculation";
$option = " -d ";
}
case 'repeat_coverage' {
$data_file = "repeat_coverage_data.txt";
$queue = "long";
$job_name = "repeat_cov";
$file_name_end = "_repeat";
$script = "repeat_coverage_calc.pl";
$script_title = "repeat coverage calculation";
$option = " -d ";
}
case 'gene_density' {
for (my $i=0; $i<$host_count;$i++) {
push(@cmd, "bsub -q normal -J gene_density -oo ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_gene.out -eo ".$outdir. "/core_dbs_".$current_release."_".$host[$i]."_gene.err perl ./gene_density_calc.pl -h ".$host[$i]." -port ".$port[$i]." -u ".$user[$i]." -p ".$pass[$i]." -pattern 'core_".$current_release."'");
push(@print_message,"Submitting gene density calculation for host ".$host[$i]." to queue 'normal'. The output from this job goes to the file ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_gene.out\n");
}
}
case 'seq_region_stats_gene' {
for (my $i=0; $i<$host_count;$i++) {
push(@cmd, "bsub -q normal -J seqreg_stats -oo ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_seqreg_gene.out -eo ".$outdir. "/core_dbs_".$current_release."_".$host[$i]."_seqreg_gene.err perl ./seq_region_stats.pl -h ".$host[$i]." -port ".$port[$i]." -u ".$user[$i]." -p ".$pass[$i]." -pattern 'core_".$current_release."' -s gene");
push(@print_message,"Submitting seq region gene stats for host ".$host[$i]." to queue 'normal'. The output from this job goes to the file ".$outdir."/core_dbs_".$current_release."_".$host[$i]."_seqreg_gene.out\n");
}
}
case 'variation_density' {
$data_file = "variation_density_data.txt";
$queue = "normal";
$job_name = "var_density";
$file_name_end = "_var";
$script = "variation_density.pl";
$script_title = "variation density calculation";
$option = " -s ";
}
case 'seq_region_stats_snp' {
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$data_file = "seq_region_stats_snp_data.txt";
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$queue = "normal";
$job_name = "seqreg_stats_snp";
$file_name_end = "_seqreg_snp";
$script = "seq_region_stats.pl";
$script_title = "seq region snp stats";
$option = " -s snp -d ";
}
else { usage(); }
}
if (defined $data_file) {
open(DATAFILE, "<$data_file") or die("Failed to open file $data_file for reading\n");
while( my $line = <DATAFILE> ) {
chomp $line;
my ($db_name, $host_name) = split(/\t/,$line);
if ( $host_string =~ /$host_name/) {
#get user and password for host
my ( $index )= grep { $host[$_] =~ /$host_name/ } 0..$#host;
push(@cmd, "bsub -q ".$queue." -J ".$job_name." -oo ".$outdir."/".$db_name.$file_name_end.".out -eo ".$outdir."/".$db_name.$file_name_end.".err perl ./".$script." -h ".$host_name." -port ".$port[$index]." -u ".$user[$index]." -p ".$pass[$index].$option. $db_name);
push(@print_message,"Submitting ".$script_title." for ".$db_name ." on host ".$host_name." to queue '".$queue."'. The output from this job goes to the file ".$outdir."/".$db_name.$file_name_end.".out\n");
}
else {
$error = 1;
$error_message{$host_name} = "Host info for $host_name not found in the script's arguments. Please run the script again providing the user and password for host $host_name.\n";
}
}
close DATAFILE;
}
#submit jobs to the farm
if ($error) {
foreach my $host_in_error (sort(keys %error_message)) {
print $error_message{$host_in_error};
}
} else {
my $cmd_count = 0;
foreach my $cmd (@cmd) {
print $print_message[$cmd_count];
#for testing
#print "\n\n". $cmd . "\n\n";
exec($cmd);
$cmd_count++;
}
}
}
sub usage {
my $indent = ' ' x length($0);
print <<EOF; exit(0);
The script lists databases/species which should have density features updated at the specified stage in the release cycle. There's an option for submitting a selected script.
Usage:
$0 -h host [-h host]* -u user [-u user]* -p password [-p password]*
$indent -port port [-port port]*
$indent [-g] [-s script name]
$indent [-o output directory path]
$indent [-help]
-h|host Database host (multiple hosts can be specified)
-u|user Database user (each host needs a user specified)
-p|pass User password (each host needs a password specified)
-port Database port (default 3306)
-g|getdbs Use this option to generate input files for the -submit option
-s|submit Use this option to submit a density feature script to the farm:
gene_gc - the script will run on all core databases
percent_gc - the script will run on dbs listed in ./percent_gc_data.txt
repeat_coverage - the script will run on dbs listed in ./repeat_coverage_data.txt
gene_density - the script will run on all core databases
seq_region_stats_gene - the script will run on all core databases
variation_density - the script will run for species listed in ./variation_density_data.txt
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seq_region_stats_snp - the script will run on dbs listed in ./seq_region_stats_snp_data.txt