diff --git a/misc-scripts/gene_gc.pl b/misc-scripts/gene_gc.pl
deleted file mode 100644
index 38fdd7d04950bdc1a5b467d3ad7904dc39863b05..0000000000000000000000000000000000000000
--- a/misc-scripts/gene_gc.pl
+++ /dev/null
@@ -1,137 +0,0 @@
-#!/usr/bin/env perl
-# Calculate per-gene GC content and store as gene attributes
-
-use warnings;
-use strict;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Utils::CliHelper;
-
-my $cli_helper = Bio::EnsEMBL::Utils::CliHelper->new();
-
-# get the basic options for connecting to a database server
-my $optsd = $cli_helper->get_dba_opts();
-# add the print option
-push( @{$optsd}, "print" );
-# process the command line with the supplied options plus a help subroutine
-my $opts = $cli_helper->process_args( $optsd, \&usage );
-
-# use the command line options to get an array of database details
-for my $db_args ( @{ $cli_helper->get_dba_args_for_opts($opts) } ) {
-
- # use the args to create a DBA
- my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$db_args} );
-
- print STDOUT "Processing species "
- . $dba->species_id()
- . " from database "
- . $dba->dbc()->dbname()
- . " on server "
- . $dba->dbc()->host() . "\n";
- delete_existing($dba) unless ( $opts->{print} );
-
- print STDOUT "Calculating Gene GC attributes\n";
- my $attribute_adaptor = $dba->get_AttributeAdaptor();
- my $total_count = 0;
- for my $gene ( @{ $dba->get_GeneAdaptor()->fetch_all() } ) {
- my $gc = $gene->feature_Slice()->get_base_count->{'%gc'};
- if ( !$opts->{print} ) {
- # attribute types need to be propagated from production database to all dbs
- # if the type exists it won't be overwritten
- my $attribute =
- Bio::EnsEMBL::Attribute->new(
- -CODE => 'GeneGC',
- -NAME => 'Gene GC',
- -DESCRIPTION => 'Percentage GC content for this gene',
- -VALUE => $gc );
- my @attributes = ($attribute);
- $attribute_adaptor->store_on_Gene( $gene->dbID, \@attributes );
- $total_count++;
- } else {
- print $gene->stable_id() . " " . $gc . "\n";
- }
- }
-
- if ( !$opts->{print} ) {
- print STDOUT "Written $total_count 'GeneGC' gene attributes to species "
- . $dba->species_id()
- . " from database "
- . $dba->dbc()->dbname()
- . " on server "
- . $dba->dbc()->host() . "\n";
- }
-
-} ## end for my $db_args ( @{ $cli_helper...})
-
-# ----------------------------------------------------------------------
-
-sub delete_existing {
-
- my $dba = shift;
-
- print STDOUT "Deleting existing 'GeneGC' gene attributes\n";
- $dba->dbc()->sql_helper()->execute_update(
- -SQL =>
-q/DELETE ga FROM gene_attrib ga, attrib_type at, gene g, seq_region s, coord_system c
-WHERE at.attrib_type_id=ga.attrib_type_id AND at.code='GeneGC'
-AND ga.gene_id=g.gene_id AND g.seq_region_id=s.seq_region_id
-AND c.coord_system_id=s.coord_system_id AND c.species_id=?
-/,
- PARAMS => [ $dba->species_id() ] );
-
- return;
-}
-
-sub usage {
- my $indent = ' ' x length($0);
- print <<EOF; exit(0);
-
-What does it do?
-
-This script calculates per-gene GC content and stores it as gene attributes.
-It deletes existing Gene GC attributes. Then fetches all genes in the
-core db and calculates the %gc for each gene.
-
-Input data: dna sequence
-Output tables: gene_attrib
-
-
-When to run it in the release cycle?
-
-It can be run whenever the genes and sequence are stable, i.e. any time after
-the genebuild handover, but before the handover to Mart.
-
-
-Which databases to run it on?
-
-It needs to be run across all core databases for every release.
-
-
-How long does it take?
-
-It takes a total of about 10 hours to run for all core databases in normal queue,
-
-
-Usage:
-
- $0 -h host [-port port] -u user -p password \\
- $indent -pattern pattern [-print] \\
- $indent [-help] \\
-
- -h|host Database host to connect to
-
- -port Database port to connect to (default 3306)
-
- -u|user Database username
-
- -p|pass Password for user
-
- -pattern Database name regexp
-
- -print Just print, don't insert or delete attributes
-
- -help This message
-
-
-EOF
-
-} ## end sub usage
diff --git a/misc-scripts/translation_attribs.pl b/misc-scripts/translation_attribs.pl
deleted file mode 100644
index c280a922f462229f202ddb0566f7e3ae73bac9fa..0000000000000000000000000000000000000000
--- a/misc-scripts/translation_attribs.pl
+++ /dev/null
@@ -1,247 +0,0 @@
-#!/software/bin/perl
-
-=head1 NAME
-
-translation_attribs.pl - script to calculate peptide statistics and store
- them in translation_attrib table
-
-=head1 SYNOPSIS
-
-translation_attribs.pl [arguments]
-
-Required arguments:
-
- --user=user username for the database
-
- --pass=pass password for database
-
-
-Optional arguments:
-
- --pattern=pattern calculate translation attribs for databases matching pattern
- Note that this is a standard regular expression of the
- form '^[a-b].*core.*' for all core databases starting with a or b
-
- --binpath=PATH directory where the binary script to calculate
- pepstats is stored (default: /software/pubseq/bin/emboss)
-
- --tmpdir=dir directory to store tmp results of pepstats (default=/tmp)
-
- --host=host server where the core databases are stored (default: ens-staging)
-
- --dbname=dbname if you want a single database to calculate the pepstats
- (all databases by default)
-
- --port=port port (default=3306)
-
- --help print help (this message)
-
-=head1 DESCRIPTION
-
-This script will calculate the peptide statistics for all core databases in the server
-and store them as a translation_attrib values
-
-=head1 EXAMPLES
-
-Calculate translation_attributes for all core databases in ens-staging
-
- $ ./translation_attribs.pl --user ensadmin --pass password
-
-Calculate translation_attributes for core databases starting with [a-c] in ens-staging (output LSF to PWD)
-
- $ ./translation_attribs.pl --user ensadmin --pass password --pattern '^[a-c].*core_50.*'
-
-Calculate translation_attribs for a single database in a ens-genomics1
-
- $ ./translation_attribs.pl --host ens-genomics1 --user ensadmin --pass password --dbname my_core_db
-
-=head1 LICENCE
-
-This code is distributed under an Apache style licence. Please see
-http://www.ensembl.org/info/about/code_licence.html for details.
-
-=head1 AUTHOR
-
-Daniel Rios <dani@ebi.ac.uk>, Ensembl core API team
-
-=head1 CONTACT
-
-=cut
-
-use strict;
-use warnings;
-use Getopt::Long;
-use Pod::Usage;
-use Bio::EnsEMBL::Translation;
-use Bio::EnsEMBL::Registry;
-use Bio::EnsEMBL::Attribute;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Data::Dumper;
-use DBI;
-use Bio::EnsEMBL::Utils::Exception qw(throw);
-use Bio::EnsEMBL::Utils::CliHelper;
-
-my $cli_helper = Bio::EnsEMBL::Utils::CliHelper->new();
-
-# get the basic options for connecting to a database server
-my $optsd = $cli_helper->get_dba_opts();
-# add the print option
-push( @{$optsd}, "binpath:s" );
-push( @{$optsd}, "tmpdir:s" );
-push( @{$optsd}, "verbose|v" );
-# process the command line with the supplied options plus a help subroutine
-my $opts = $cli_helper->process_args( $optsd, \&pod2usage );
-
-$opts->{binpath} ||= '/software/pubseq/bin/emboss';
-$opts->{tmpdir} ||= '/tmp';
-$opts->{port} ||= '3306';
-$opts->{host} ||= 'ens-staging';
-$opts->{user} ||= 'ensro';
-$opts->{pattern} ||= qr/.+_core_.+/;
-
-my %PEPSTATS_CODES = ( 'Number of residues' => 'NumResidues',
- 'Molecular weight' => 'MolecularWeight',
- 'Ave. residue weight' => 'AvgResWeight',
- 'Charge' => 'Charge',
- 'Isoelectric point' => 'IsoPoint'
- );
-
-my %MET_AND_STOP = ( 'Starts with methionine' => 'starts_met',
- 'Contains stop codon' => 'has_stop_codon'
- );
-
-
-
-my %attributes_to_delete = (%PEPSTATS_CODES);
-my $translation_attribs = {};
-my $translation;
-my $dbID;
-
-# use the command line options to get an array of database details
-for my $db_args ( @{ $cli_helper->get_dba_args_for_opts($opts) } ) {
-
- # use the args to create a DBA
- my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$db_args} );
- my $dbname = $dba->dbc()->dbname();
- print STDOUT "Processing species "
- . $dba->species_id()
- . " from database "
- . $dba->dbc()->dbname()
- . " on server "
- . $dba->dbc()->host() . "\n";
-
- if ( $dbname =~ /(vega|otherfeatures)/ ) {
- my $other_dbname = $dbname;
- $other_dbname =~ s/$1/core/;
-
- $opts->{dbname} = $other_dbname;
- #for vega and otherfeatures databases, add the core as the dna database
- my $core_db = Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$db_args}, -DBNAME => $other_dbname, -GROUP => 'core' );
- $dba->dnadb($core_db);
- }
-
- print "Removing attributes from database ", $dba->dbc->dbname, "\n";
- remove_old_attributes( $dba, \%attributes_to_delete);
- my $translationAdaptor = $dba->get_TranslationAdaptor();
- my $attributeAdaptor = $dba->get_AttributeAdaptor();
- print
- "Going to update translation_attribs in",
- $dba->dbc->dbname, "\n";
-
-#for all the translations in the database, run pepstats and update the translation_attrib table
- my @translation_ids = @{
- $dba->dbc()->sql_helper()->execute_simple(
--SQL=>"SELECT tl.translation_id FROM translation tl, transcript tr, seq_region s, coord_system c WHERE tl.transcript_id = tr.transcript_id AND tr.seq_region_id = s.seq_region_id AND s.coord_system_id = c.coord_system_id AND c.species_id = ? order by tl.translation_id",
- -PARAMS=>[$dba->species_id()] ) };
- my $tmpfile = $opts->{tmpdir} . "/$$.pep";
- open( TMP, "> $tmpfile" ) || warn "PEPSTAT: $!";
- print "Retrieving translations\n";
- for my $dbID (@translation_ids) {
-
- #foreach translation, retrieve object
- my $translation = $translationAdaptor->fetch_by_dbID($dbID);
- if ( $opts->{verbose} ) {
- print "Dumping translation dbID, $dbID...\n";
- }
- my $peptide_seq = $translation->seq();
- if ( !( $peptide_seq =~ m/[BZX]/ig ) ) {
- if ( $peptide_seq !~ /\n$/ ) { $peptide_seq .= "\n" }
- $peptide_seq =~ s/\*$//;
- print TMP ">$dbID\n$peptide_seq";
- } else {
- print "Skipping translation dbID $dbID due to ambiguity codes...\n";
- }
- }
- close(TMP);
- print "Running pepstat\n";
-
- my $PEPSTATS = $opts->{binpath} . '/bin/pepstats';
- throw("pepstats binary at $PEPSTATS cannot be executed")
- if ( !-x $PEPSTATS );
- open( OUT, "$PEPSTATS -filter < $tmpfile 2>&1 |" )
- || warn "PEPSTAT: $!";
- my @lines = <OUT>;
- close(OUT);
- unlink($tmpfile);
- my $attribs = {};
- my $tId;
- print "Parsing pepstat\n";
-
- foreach my $line (@lines) {
- if ( $line =~ /PEPSTATS of ([^ ]+)/ ) {
- $tId = $1;
- } elsif ( defined $tId ) {
- if ( $line =~ /^Molecular weight = (\S+)(\s+)Residues = (\d+).*/ ) {
- $attribs->{$tId}{'Number of residues'} = $3;
- $attribs->{$tId}{'Molecular weight'} = $1;
- } elsif ( $line =~
-/^Average(\s+)(\S+)(\s+)(\S+)(\s+)=(\s+)(\S+)(\s+)(\S+)(\s+)=(\s+)(\S+)/ )
- {
- $attribs->{$tId}{'Ave. residue weight'} = $7;
- $attribs->{$tId}{'Charge'} = $12;
- } elsif ( $line =~ /^Isoelectric(\s+)(\S+)(\s+)=(\s+)(\S+)/ ) {
- $attribs->{$tId}{'Isoelectric point'} = $5;
- } elsif ( $line =~ /FATAL/ ) {
- print STDERR "pepstats: $line\n";
- }
- }
- }
- for my $id ( keys %$attribs ) {
- my $aas = $attribs->{$id};
- if ( $opts->{verbose} ) {
- print "Storing attribs for translation dbID, $id...\n";
- }
- store_translation_attrib( $attributeAdaptor, $id, $aas );
- }
-} ## end for my $db_args ( @{ $cli_helper...})
-
-#will remove any entries in the translation_attrib table for the attributes, if any
-#this method will try to remove the old starts_met and has_stop_codon attributes, if present
-#this is to allow to be run on old databases, but removing the not used attributes
-sub remove_old_attributes {
- my $dba = shift;
- my $attributes = shift;
- print "removing all translation attributes for db, "
- . $dba->{_dbc}->{_dbname} . "\n";
- foreach my $value ( values %{$attributes} ) {
- my $sql = "delete ta FROM translation_attrib ta, attrib_type at, translation tl, transcript tr, seq_region s, coord_system c WHERE at.attrib_type_id = ta.attrib_type_id AND ta.translation_id=tl.translation_id and tl.transcript_id = tr.transcript_id AND tr.seq_region_id = s.seq_region_id AND s.coord_system_id = c.coord_system_id AND c.species_id = ? and at.code=?";
- $dba->dbc()->sql_helper()->execute_update(-SQL=>$sql,-PARAMS=>[$dba->species_id(),$value]);
- }
- return;
-
-} ## end sub remove_old_attributes
-
-sub store_translation_attrib {
- my ( $attributeAdaptor, $translation, $attribs ) = @_;
- my @attribs;
- for my $key ( keys %$attribs ) {
- my $value = $attribs->{$key};
- push @attribs,
- Bio::EnsEMBL::Attribute->new( '-code' => $PEPSTATS_CODES{$key},
- '-name' => $key,
- '-value' => $value );
- }
- $attributeAdaptor->store_on_Translation( $translation, \@attribs );
- return;
-}
-
diff --git a/misc-scripts/translation_attribs_wrapper.pl b/misc-scripts/translation_attribs_wrapper.pl
deleted file mode 100644
index d6c25d81dfe0726beab380a68d179fff669a1b14..0000000000000000000000000000000000000000
--- a/misc-scripts/translation_attribs_wrapper.pl
+++ /dev/null
@@ -1,158 +0,0 @@
-#!/usr/local/ensembl/bin/perl
-
-=head1 NAME
-
-translation_attribs_wrapper.pl
-
-Script to calculate peptide statistics and store them in
-translation_attrib table. This is mainly a wrapper around the
-translation_attribs.pl script to submit several jobs to the farm.
-
-=head1 SYNOPSIS
-
-translation_attribs_wrapper.pl [arguments]
-
-Required arguments:
-
- --user=user username for the database
-
- --pass=pass password for database
-
- --release=release release number
-
-Optional arguments:
-
- --binpath=PATH directory where the binary script to
- calculate pepstats is stored (default:
- /software/pubseq/bin/emboss)
-
- --tmpdir=directory directory to store temporary results of pepstats
- (default: /tmp)
-
- --host=host server where the core databases are stored
- (default: ens-staging)
-
- --port=port port (default: 3306)
-
- --path=path path where the LSF output will be stored
- (default: the current directory)
-
- --help display help (this message)
-
-=head1 DESCRIPTION
-
-This script will calculate the peptide statistics for all core databases
-in the server and store them as a translation_attrib values. This is a
-wraper around the translation_attrib and will simply submit jobs to the
-farm grouping the core databases in patterns.
-
-=head1 EXAMPLES
-
-Calculate translation_attributes for all databases in ens-staging
-
- $ ./translation_attribs_wrapper.pl --user ensadmin \
- --pass password --release 51 --path /my/path/to/lsf/output
-
-=head1 LICENCE
-
-This code is distributed under an Apache style licence. Please see
-http://www.ensembl.org/info/about/code_licence.html for details.
-
-=head1 AUTHOR
-
-Daniel Rios <dani@ebi.ac.uk>, Ensembl core API team
-
-=head1 CONTACT
-
-=cut
-
-use strict;
-use warnings;
-
-use Getopt::Long;
-use Pod::Usage;
-
-use Bio::EnsEMBL::Utils::Exception qw(throw);
-
-
-## Command line options
-
-my $binpath = "'/software/pubseq/bin/emboss'";
-my $tmpdir = "'/tmp'";
-my $host = "ens-staging";
-my $path = $ENV{PWD};
-my $release = undef;
-my $user = undef;
-my $pass = undef;
-my $port = 3306;
-my $help = undef;
-
-GetOptions('binpath=s' => \$binpath,
- 'tmpdir=s' => \$tmpdir,
- 'host=s' => \$host,
- 'user=s' => \$user,
- 'pass=s' => \$pass,
- 'port=s' => \$port,
- 'release=i' => \$release,
- 'path=s' => \$path,
- 'help' => \$help
- );
-
-pod2usage(1) if($help);
-throw("--user argument required") if (!defined($user));
-throw("--pass argument required") if (!defined($pass));
-throw("--release argument required") if (!defined($release));
-
-my $queue = 'long';
-my $memory = "'select[mem>4000] rusage[mem=4000]' -M4000000";
-my $options = '';
-if (defined $binpath){
- $options .= "--binpath $binpath ";
-}
-if (defined $tmpdir){
- $options .= "--tmpdir $tmpdir "
-}
-if (defined $host){
- $options .= "--host $host ";
-}
-if (defined $port){
- $options .= "--port $port ";
-}
-
-my @ranges = ('^[a-b]','^c','^d','^e','^f','^[g-h]','^[i-l]','^m[a-i]','^m[j-z]','^[n-o]','^p','^[q-r]','^[s-t]','^[u-z]');
-my $core_db = ".*core_$release\_.*";
-my $call;
-foreach my $pattern (@ranges){
- $call = "bsub "
- . "-R 'select[(myens_staging1<=800)&&(myens_staging2<=800)]' "
- . "-o ${path}/output_translation_${pattern}.txt "
- . "-e ${path}/output_translation_${pattern}.err "
- . "-q $queue "
- . "-R$memory "
- . "perl ./translation_attribs.pl --user $user --pass $pass $options";
- $call .= " --pattern '" . $pattern . $core_db . "'";
-
- system($call);
-#print $call,"\n";
-}
-
-#we now need to run it for the otherfeatures|vega databases, but only the pepstats
-
-my $vega_db = ".*_vega_$release\_.*";
-$call = "bsub -R 'select[(myens_staging1<=800)&&(myens_staging2<=800)]' -o '" . "$path/output_translation_vega.txt" . "' -q $queue -R$memory perl ./translation_attribs.pl --user $user --pass $pass $options";
-$call .= " --pattern '" . $vega_db. "'";
-
-system($call);
-#print $call,"\n";
-
-@ranges = ('^[a-b]','^c','^[d-e]','^[f-h]','^[i-m]','^[n-o]','^p','^[q-s]','^[t-z]');
-
-my $other_db = ".*_otherfeatures_$release\_.*";
-
-foreach my $pattern (@ranges){
- $call = "bsub -R 'select[(myens_staging1<=800)&&(myens_staging2<=800)]' -o '" . "$path/output_translation_other_$pattern.txt" . "' -q $queue -R$memory perl ./translation_attribs.pl --user $user --pass $pass $options";
- $call .= " --pattern '" . $pattern . $other_db. "'";
-
- system($call);
-#print $call,"\n";
-}