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Commit e253c783 authored by Ian Longden's avatar Ian Longden
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pod added

parent 02a80c53
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......@@ -8,6 +8,7 @@ use IPC::Open3;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Translation;
use XrefMapper::db;
use vars '@ISA';
=head1 NAME
......@@ -520,6 +521,17 @@ sub method{
return $self->{_method};
}
=head2 core
Arg [1] : (optional)
Example : $mapper->core($new_core);
Description: Getter / Setter for the core.
info for the ensembl core database.
Returntype : XrefMapper::db
Exceptions : none
=cut
sub core{
my ($self, $arg) = @_;
......@@ -528,6 +540,19 @@ sub core{
return $self->{_core};
}
=head2 dumpcheck
Arg [1] : (optional)
Example : $mapper->dumpcheck("yes");
Description: Getter / Setter for dumpcheck.
If set the mapper will not dump fasta files
if they exist already.
Returntype : scalar
Exceptions : none
=cut
sub dumpcheck {
my ($self, $arg) = @_;
......@@ -536,6 +561,18 @@ sub dumpcheck {
return $self->{_dumpcheck};
}
=head2 maxdump
Arg [1] : (optional)
Example : $mapper->maxdump(10);
Description: Getter / Setter for maxdump.
If set the mapper will only dump that number of
sequences into the fasta files. (Mainly used for testing).
Returntype : scalar
Exceptions : none
=cut
sub maxdump {
my ($self, $arg) = @_;
......@@ -544,6 +581,20 @@ sub maxdump {
return $self->{_maxdump};
}
=head2 use_existing_mappings
Arg [1] : (optional)
Example : $mapper->use_existing_mappings("yes");
Description: Getter / Setter for use_existing_mappings.
If set the mapper will not redo the mapping
but parse the existing .map files.
Returntype : scalar
Exceptions : none
=cut
sub use_existing_mappings {
my ($self, $arg) = @_;
......@@ -552,6 +603,18 @@ sub use_existing_mappings {
return $self->{_use_existing_mappings};
}
=head2 xref
Arg [1] : (optional)
Example : $mapper->core($new_core);
Description: Getter / Setter for the core.
info for the xref database.
Returntype : XrefMapper::db
Exceptions : none
=cut
sub xref{
my ($self, $arg) = @_;
......@@ -560,6 +623,8 @@ sub xref{
return $self->{_xref};
}
=head2 run_mapping
Arg[1] : List of lists of (method, query, target)
......@@ -577,7 +642,7 @@ sub run_mapping {
my ($self, $lists) = @_;
# delete old output files in target directory if we're going to produce new ones
if (!defined($self->use_existing_mappings)) {
if (!defined($self->use_existing_mappings())) {
my $dir = $self->core->dir();
unlink (<$dir/*.map $dir/*.out $dir/*.err>);
}
......@@ -710,8 +775,6 @@ sub submit_depend_job {
=head2 parse_mappings
Arg[1] : The target file used in the exonerate run. Used to work out the Ensembl object type.
Arg[2] :
Example : none
Description: Parse exonerate output files and build files for loading into target db tables.
Returntype : List of strings
......@@ -791,8 +854,8 @@ sub parse_mappings {
# get or create the appropriate analysis ID
# XXX restore when using writeable database
#my $analysis_id = $self->get_analysis_id($type);
my $analysis_id = 999;
my $analysis_id = $self->get_analysis_id($type);
# my $analysis_id = 999;
while (<FILE>) {
......@@ -1105,8 +1168,8 @@ sub get_analysis_id {
my ($self, $ensembl_type) = @_;
my %typeToLogicName = ( 'dna' => 'XrefExonerateDNA',
'protein' => 'XrefExonerateProtein' );
my %typeToLogicName = ( 'transcript' => 'XrefExonerateDNA',
'translation' => 'XrefExonerateProtein' );
my $logic_name = $typeToLogicName{lc($ensembl_type)};
......@@ -1118,7 +1181,7 @@ sub get_analysis_id {
if (my @row = $sth->fetchrow_array()) {
$analysis_id = $row[0];
print "Found exising analysis ID ($analysis_id) for $logic_name\n";
# print "Found exising analysis ID ($analysis_id) for $logic_name\n";
} else {
......@@ -1770,7 +1833,7 @@ sub do_upload {
}
print "Setting $table display_xrefs from $file\n";
my $str = "mysql -u " .$core_db->user() ." -p" . $core_db->password() . " -h " . $core_db->host() ." -P " . $core_db->port() . " " .$core_db->dbname() . " < $file";
my $str = "mysql -u " .$core_db->username() ." -p" . $core_db->password() . " -h " . $core_db->host() ." -P " . $core_db->port() . " " .$core_db->dbname() . " < $file";
system $str;
#$sth = $core_db->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
......
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