SeqStoreConverter::vega::DanioRerio Class Reference
Public Member Functions | |
| public | copy_internal_clone_names () |
| public | update_clone_info () |
Detailed Description
Definition at line 5 of file DanioRerio.pm.
Member Function Documentation
◆ copy_internal_clone_names()
| public SeqStoreConverter::vega::DanioRerio::copy_internal_clone_names | ( | ) |
Undocumented method
Code:
click to view
my $self = shift;
my $target = $self->target();
my $source = $self->source();
my $dbh = $self->dbh();
$self->debug("Vega danio specific - copying internal clone names to seq_region_attrib");
#get id for 'fpc_clone_id' attribute
$dbh->do("INSERT INTO $target.attrib_type (code,name,description)".
"values ('fpc_clone_id','fpc clone','clone id used for linking to Zebrafish webFPC')");
my ($attrib_id) = $dbh->selectrow_array("Select attrib_type_id from $target.attrib_type where code = 'fpc_clone_id'");
warn "No attrib id found\n" unless defined($attrib_id);
#get clone details
my $select1_sth = $dbh->prepare
("SELECT seq_region_id, name from $target.seq_region where coord_system_id = 3;");
$select1_sth->execute();
my ($seq_region_id, $embl_name);
$select1_sth->bind_columns(\$seq_region_id, \$embl_name);
my $clone_name;
my $select2_sth = $dbh->prepare("select name from $source.clone where embl_acc= ?");
my $insert_sth = $dbh->prepare("insert into $target.seq_region_attrib values (?,$attrib_id,?)");
while ($select1_sth->fetch()) {
$embl_name =~ s/([\d\w]+).*/$1/;
$select2_sth->bind_param(1,$embl_name);
$select2_sth->execute;
$insert_sth->bind_param(1,$seq_region_id);
while (my ($clone_name) = $select2_sth->fetchrow_array()) {
$insert_sth->bind_param(2,$clone_name);
$insert_sth->execute();
}
}
}
◆ update_clone_info()
| public SeqStoreConverter::vega::DanioRerio::update_clone_info | ( | ) |
Undocumented method
Code:
click to view
sub update_clone_info {
my $self = shift;
my $target_cs_name = shift;
my $target = $self->target();
my $source = $self->source();
my $dbh = $self->dbh();
# clone_info, current_clone_info
$self->debug("Vega Danio_specific - Transforming clone_id into seq_region_id for clone_info and current_clone_info");
foreach my $table_name ('clone_info','current_clone_info') {
my $select_st1 =
"SELECT ctg.name, ctg.clone_id " .
"FROM $source.contig ctg, $source.$table_name ci " .
"WHERE ctg.clone_id = ci.clone_id " .
"AND ctg.name not like 'ctg%' " .
"AND ctg.name not like 'NA%'";
my $query_results1 = $dbh->selectall_arrayref($select_st1);
my $i = 0;
foreach my $contig_name (@$query_results1) {
my $embl_acc = $contig_name->[0];
my $select_st2 =
"SELECT sr.seq_region_id " .
"FROM $target.seq_region sr " .
"WHERE sr.name = '$embl_acc'";
my @query_results2 = $dbh->selectrow_array($select_st2);
push @{$query_results1->[$i]},@query_results2;
$i++;
}
foreach my $clone (@$query_results1) {
my $seq_reg_id = $clone->[2];
my $clone_id = $clone->[1];
my $update_query =
"UPDATE $target.$table_name " .
"SET clone_id = '$seq_reg_id' " .
"WHERE clone_id = '$clone_id'";
$dbh->do($update_query);
}
my $alter_struct_1 =
"ALTER table $target.$table_name " .
"CHANGE clone_id seq_region_id int(10) not null";
my $alter_struct_2 =
"ALTER table $target.$table_name " .
"add unique index (seq_region_id)";
$dbh->do($alter_struct_1);
$dbh->do($alter_struct_2);
}
# assembly_tag
$self->debug("Vega Danio_specific - Transforming contig_id into seq_region_id for assembly_tag");
# first remove orphans from assembly_tag table (i.e. entries pointing to
# non-existing contigs)
my $numrows = $dbh->do(qq(
DELETE at
FROM $source.assembly_tag at
LEFT JOIN $source.contig c ON c.contig_id = at.contig_id
WHERE c.contig_id IS NULL
));
$self->debug(" Deleted $numrows orphans from assembly_tag");
my $select_st3 =
"SELECT ctg.name, ctg.contig_id " .
"FROM $source.contig ctg, $source.assembly_tag at " .
"WHERE ctg.contig_id = at.contig_id " .
"AND ctg.name not like 'ctg%' " .
"AND ctg.name not like 'NA%'";
my $query_results3 = $dbh->selectall_arrayref($select_st3);
my $j = 0;
foreach my $contig_name (@$query_results3) {
my $embl_acc = $contig_name->[0];
my $select_st4 =
"SELECT sr.seq_region_id " .
"FROM $target.seq_region sr " .
"WHERE sr.name = '$embl_acc'";
my @query_results4 = $dbh->selectrow_array($select_st4);
push @{$query_results3->[$j]}, @query_results4;
$j++;
}
foreach my $contig (@$query_results3) {
my $seq_reg_id = $contig->[2];
my $contig_id = $contig->[1];
my $update_query =
"UPDATE $target.assembly_tag " .
"SET contig_id = '$seq_reg_id' " .
"WHERE contig_id = '$contig_id'";
$dbh->do($update_query);
}
$dbh->do(" ALTER TABLE $target.assembly_tag
CHANGE contig_id seq_region_id int(10) UNSIGNED NOT NULL");
$dbh->do(" ALTER TABLE $target.assembly_tag
CHANGE contig_start seq_region_start int(10)");
$dbh->do(" ALTER TABLE $target.assembly_tag
CHANGE contig_end seq_region_end int(10)");
$dbh->do(" ALTER TABLE $target.assembly_tag
CHANGE contig_strand seq_region_strand tinyint(1)");
}
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/surgery/SeqStoreConverter/vega/DanioRerio.pm
