Commit 56de3cde authored by Ian Longden's avatar Ian Longden
Browse files

Add PRINTS back as it is needed for the protein alignments but store the...

Add PRINTS back as it is needed for the protein alignments but store the source in the  interpro table as this is usefull information, that allows us to ignore PRINTS later.
parent d24ec3a8
......@@ -46,7 +46,7 @@ sub run {
my $add_interpro_sth =
$self->dbi()
->prepare("INSERT INTO interpro (interpro, pfam) VALUES(?,?)");
->prepare("INSERT INTO interpro (interpro, pfam, dbtype ) VALUES(?,?,?)");
my $get_interpro_sth =
$self->dbi()
......@@ -59,11 +59,6 @@ sub run {
. "(accession,version,label,description,source_id,species_id, info_type) "
. "VALUES(?,?,?,?,?,?,?)" );
# my $get_xref_sth =
# $self->dbi()
# ->prepare( "SELECT xref_id FROM xref "
# . "WHERE accession = ? AND source_id = ?" );
my $dir = dirname($file);
my %short_name;
......@@ -112,16 +107,16 @@ sub run {
my ($members) = $_ =~ /<member_list>(.+)<\/member_list>/s;
while ( $members =~
/db="(PROSITE|PFAM|PREFILE|PROFILE|TIGRFAMs|PIRSF|SMART|SSF)"\s+dbkey="(\S+)"/cgm
/db="(PROSITE|PFAM|PREFILE|PROFILE|TIGRFAMs|PRINTS|PIRSF|SMART|SSF)"\s+dbkey="(\S+)"/cgm
)
{
my ( $db_type, $id ) = ( $1, $2 );
if( $db_type eq 'SSF' ){ $id =~ s/^SSF// } # Strip SSF prefix
if ( !$self->get_xref( $interpro, $id, $species_id ) ) {
$add_interpro_sth->execute( $interpro, $id );
$count{$db_type}++;
}
# if ( !$self->get_xref( $interpro, $id, $species_id ) ) {#no idea why if was checking for something with source of the name it would never work
$add_interpro_sth->execute( $interpro, $id, $db_type );
$count{$db_type}++;
# }
}
}
}
......@@ -158,14 +153,4 @@ sub run {
return 0;
}
#sub get_xref{
# my ($get_xref_sth, $acc, $source) = @_;
#
# $get_xref_sth->execute($acc, $source) || die "FAILED $acc $source\n";
# if(my @row = $get_xref_sth->fetchrow_array()) {
# return $row[0];
# }
# return 0;
#}
1;
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