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Commit 0815b0b7 authored by Ian Longden's avatar Ian Longden
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curated_transcriptParser now replaces HGNC and MGI variants as it was... 

curated_transcriptParser now replaces HGNC and MGI variants as it was basically the same code in both
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misc-scripts/xref_mapping/XrefParser/MGI_curated_transcriptParser.pm deleted 100644 → 0
+ 0
− 175
View file @ 1add959d
package XrefParser::MGI_curated_transcriptParser;
use strict;
use File::Basename;
use Bio::EnsEMBL::Registry;
use base qw( XrefParser::BaseParser );
my $reg = "Bio::EnsEMBL::Registry";
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print STDERR "\nUsage: MGI_curated_transcriptParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
run(@ARGV);
}
sub run_script {
my $self = shift if (defined(caller(1)));
my $file = shift;
my $source_id = shift;
my $species_id = shift;
my $verbose = shift;
my ($type, $my_args) = split(/:/,$file);
my $vuser ="ensro";
my $vhost;
my $vport;
my $vdbname;
my $vpass;
my $cuser ="ensro";
my $chost;
my $cport;
my $cdbname;
my $cpass;
my $host = "ens-staging2";
my $user = "ensro";
if($my_args =~ /host[=][>](\S+?)[,]/){
$host = $1;
}
if($my_args =~ /user[=][>](\S+?)[,]/){
$user = $1;
}
if($my_args =~ /vhost[=][>](\S+?)[,]/){
$vhost = $1;
}
if($my_args =~ /vport[=][>](\S+?)[,]/){
$vport = $1;
}
if($my_args =~ /vdbname[=][>](\S+?)[,]/){
$vdbname = $1;
}
if($my_args =~ /vpass[=][>](\S+?)[,]/){
$vpass = $1;
}
if($my_args =~ /vuser[=][>](\S+?)[,]/){
$vuser = $1;
}
if($my_args =~ /chost[=][>](\S+?)[,]/){
$chost = $1;
}
if($my_args =~ /cport[=][>](\S+?)[,]/){
$cport = $1;
}
if($my_args =~ /cdbname[=][>](\S+?)[,]/){
$cdbname = $1;
}
if($my_args =~ /cpass[=][>](\S+?)[,]/){
$cpass = $1;
}
if($my_args =~ /cuser[=][>](\S+?)[,]/){
$cuser = $1;
}
my $vega_dbc;
my $core_dbc;
if(defined($vdbname)){
print "Using $host $vdbname for Vega and cdbname for Core\n";
$vega_dbc = $self->dbi2($vhost, $vport, $vuser, $vdbname, $vpass);
if(!defined($vega_dbc)){
print "Problem could not open connectipn to $vhost, $vport, $vuser, $vdbname, $vpass\n";
return 1;
}
$core_dbc = $self->dbi2($chost, $cport, $cuser, $cdbname, $cpass);
if(!defined($core_dbc)){
print "Problem could not open connectipn to $chost, $cport, $cuser, $cdbname, $cpass\n";
return 1;
}
}
else{
$reg->load_registry_from_db(
-host => $host,
-user => $user);
$vega_dbc = $reg->get_adaptor("mouse","vega","slice");
if(!defined($vega_dbc)){
print "Could not connect to mouse vega database using load_registry_from_db $host $user\n";
return 1;
}
$vega_dbc = $vega_dbc->dbc;
$core_dbc = $reg->get_adaptor("mouse","core","slice");
if(!defined($core_dbc)){
print "Could not connect to mouse core database using load_registry_from_db $host $user\n";
return 1;
}
$core_dbc= $core_dbc->dbc;
}
my $clone_source_id =
$self->get_source_id_for_source_name('Clone_based_vega_transcript');
my $curated_source_id =
$self->get_source_id_for_source_name('MGI_curated_transcript');
my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
my %ott_to_vega_name;
my %ott_to_enst;
my $sth = $core_dbc->prepare($sql) || die "Could not prepare for core $sql\n";
foreach my $external_db (qw(Vega_transcript OTTT shares_CDS_and_UTR_with_OTTT shares_CDS_with_OTTT)){
$sth->execute($external_db) or croak( $core_dbc->errstr());
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[1]} = $row[0];
}
}
$sth = $vega_dbc->prepare($sql) || die "Could not prepare for vega $sql\n";
$sth->execute("Vega_transcript") or croak( $vega_dbc->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
next if ($row[1] =~ /^OTT/);
$ott_to_vega_name{$row[0]} = $row[1];
}
$sth->finish;
my $xref_count = 0;
foreach my $ott (keys %ott_to_enst){
if(defined($ott_to_vega_name{$ott})){
my $id = $curated_source_id;
my $name = $ott_to_vega_name{$ott};
$name =~ s/WU://;
if($name =~ /[.]/){
$id = $clone_source_id;
# keep it apparently $name =~ s/[.]\d+//; #remove .number
}
my $xref_id = $self->add_xref($name, "" , $name , "", $id, $species_id, "DIRECT");
$xref_count++;
$self->add_direct_xref($xref_id, $ott_to_enst{$ott}, "transcript", "");
}
}
print "$xref_count direct xrefs succesfully parsed\n" if($verbose);
return 0;
}
1;
misc-scripts/xref_mapping/XrefParser/HGNC_curated_transcriptParser.pm → misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
+ 30
− 8
View file @ 0815b0b7
package XrefParser::HGNC_curated_transcriptParser;
package XrefParser::curated_transcriptParser;
use strict;
use File::Basename;
......@@ -14,7 +14,7 @@ my $reg = "Bio::EnsEMBL::Registry";
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print STDERR "\nUsage: HGNC_curated_transcriptParser.pm file <source_id> <species_id>\n\n";
print STDERR "\nUsage: curated_transcriptParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
......@@ -40,6 +40,18 @@ sub run_script {
if($my_args =~ /user[=][>](\S+?)[,]/){
$user = $1;
}
my %id2name = $self->species_id2name;
my $species_name = $id2name{$species_id}[0];
my $source_prefix;
if($species_name eq "homo_sapiens" ){
$source_prefix = "HGNC";
}
elsif($species_name eq "mus_musculus" ){
$source_prefix = "MGI";
}
else{
die "Species is $species_name and is not homo_sapines or mus_musculus the only two valid species\n";
}
my $vuser ="ensro";
my $vhost;
......@@ -101,19 +113,27 @@ sub run_script {
}
else{
my @dbas = @{$reg->get_all_adaptors()};
foreach my $db (@dbas){
print "DB: $db\n";
}
$reg->load_registry_from_db(
-host => $host,
-user => $user);
$vega_dbc = $reg->get_adaptor("human","vega","slice");
@dbas = @{$reg->get_all_adaptors(-species => $species_name)};
# foreach my $db (@dbas){
# print "DB2: ".$db->db->group."\t$db\n";
# }
$vega_dbc = $reg->get_adaptor($species_name,"vega","slice");
if(!defined($vega_dbc)){
print "Could not connect to human vega database using load_registry_from_db $host $user\n";
print "Could not connect to $species_name vega database using load_registry_from_db $host $user\n";
return 1;
}
$vega_dbc = $vega_dbc->dbc;
$core_dbc = $reg->get_adaptor("human","core","slice");
$core_dbc = $reg->get_adaptor($species_name,"core","slice");
if(!defined($core_dbc)){
print "Could not connect to human core database using load_registry_from_db $host $user\n";
print "Could not connect to $species_name core database using load_registry_from_db $host $user\n";
return 1;
}
$core_dbc= $core_dbc->dbc;
......@@ -123,9 +143,11 @@ sub run_script {
my $clone_source_id =
$self->get_source_id_for_source_name('Clone_based_vega_transcript');
my $curated_source_id =
$self->get_source_id_for_source_name('HGNC_curated_transcript');
$self->get_source_id_for_source_name($source_prefix."_curated_transcript");
my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
print "source id is $source_id, curated_source_id is $curated_source_id\n";
my $sql = 'select tsi.stable_id, x.display_label, t.status from xref x, object_xref ox , transcript_stable_id tsi, external_db e, transcript t where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and t.transcript_id = tsi.transcript_id and e.db_name like ?';
my %ott_to_vega_name;
......
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