Raw content of XrefParser::OTTTParser
<![CDATA[package XrefParser::OTTTParser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
use strict;
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print "\nUsage: OTTTParser.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 $species_id = shift;
my ($type, $my_args) = split(/:/,$file);
my $user = "ensro";
my $host ="ens-staging";
my $port = "3306";
my $dbname = "homo_sapiens_vega_51_36m";
my $pass;
if($my_args =~ /host[=][>](\S+?)[,]/){
$host = $1;
}
if($my_args =~ /port[=][>](\S+?)[,]/){
$port = $1;
}
if($my_args =~ /dbname[=][>](\S+?)[,]/){
$dbname = $1;
}
if($my_args =~ /pass[=][>](\S+?)[,]/){
$pass = $1;
}
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_enst;
my $dbi2 = $self->dbi2($host, $port, $user, $dbname, $pass);
if(!defined($dbi2)){
return 1;
}
my $sth = $dbi2->prepare($sql); # funny number instead of stable id ?????
$sth->execute("ENST_CDS") or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[0]} = $row[1];
}
$sth->finish;
$sth = $dbi2->prepare($sql);
$sth->execute("ENST_ident") or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[0]} = $row[1];
}
$sth->finish;
my $xref_count = 0;
foreach my $ott (keys %ott_to_enst){
my $xref_id = $self->add_xref($ott, "" , $ott , "", $source_id, $species_id, "DIRECT");
$xref_count++;
$self->add_direct_xref($xref_id, $ott_to_enst{$ott}, "transcript", "");
}
}
#sub dbi2{
# my $self = shift;
# my ($host, $port, $user, $dbname, $pass) = @_;
# if ( !defined $dbi2 || !$dbi2->ping() ) {
# my $connect_string =
# sprintf( "dbi:mysql:host=%s;port=%s;database=%s",
# $host, $port, $dbname );
# $dbi2 =
# DBI->connect( $connect_string, $user, $pass,
# {
# 'RaiseError' => 1 } )
# or croak( "Can't connect to database: " . $DBI::errstr );
# $dbi2->{'mysql_auto_reconnect'} = 1; # Reconnect on timeout
# }
# return $dbi2;
#}
1;
]]>