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Commit 17b6bdff authored by Laura Clarke's avatar Laura Clarke
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Added store methods to RawContigAdaptor and CloneAdaptor, 

Added depreciated waning to write_contig, write_clone, and _insertSequence methods in DBAdaptor
Added a use Bio::LocationI statement to RepeatFeatureAdaptor as lack of it was causing complier errors
parent 607380cb
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modules/Bio/EnsEMBL/DBSQL/CloneAdaptor.pm
+ 46
− 3
View file @ 17b6bdff
......@@ -150,10 +150,10 @@ sub fetch_by_accession_version {
sub fetch_by_name {
my ($self, $name) = @_;
print $name."\n";
$self->throw("name not given") unless $name;
$self->throw("name not given");
my $clone = $self->_generic_sql_query(
my $clone = $self->_generic_sql_fetch(
qq{ WHERE name = '$name' }
);
......@@ -389,5 +389,48 @@ sub create_tables {
}
sub store{
my ($self, $clone) = @_;
$clone || $self->throw("trying to write a clone without a clone object : $!\n");
if( !$clone->isa('Bio::EnsEMBL::DB::CloneI') ) {
$self->throw("Clone '$clone' is not a 'Bio::EnsEMBL::DB::CloneI'");
}
my $sql = "insert into clone(name,
embl_acc,
version,
embl_version,
htg_phase,
created,
modified)
values( '".$clone->id."' , '".
$clone->embl_id."', ".
$clone->version.",".
$clone->embl_version.", ".
$clone->htg_phase.",
FROM_UNIXTIME(".$clone->created."),
FROM_UNIXTIME(".$clone->modified."))";
my $sth = $self->prepare($sql);
my $rv = $sth->execute();
$self->throw("Failed to insert clone $clone->id") unless $rv;
$sth = $self->prepare("select last_insert_id()");
my $res = $sth->execute;
my $row = $sth->fetchrow_hashref;
$sth->finish;
my $id = $row->{'last_insert_id()'};
foreach my $contig($clone->get_all_Contigs()){
my $rca = $self->db->get_RawContigAdaptor();
$rca->store($contig, $id);
}
}
1;
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+ 92
− 75
View file @ 17b6bdff
......@@ -545,30 +545,36 @@ sub get_object_by_wildcard{
sub write_Clone {
my ($self,$clone) = @_;
my $clone_id = $clone->id;
$clone || $self->throw("Trying to write a clone without a clone object!\n");
if( !$clone->isa('Bio::EnsEMBL::DB::CloneI') ) {
$self->throw("Clone '$clone' is not a 'Bio::EnsEMBL::DB::CloneI'");
}
$self->warn("this method is being depreciated please use Bio::EnsEMBL::CloneAdaptor->store()\n");
my $clone_ad = $self->get_CloneAdaptor();
$clone_ad->store($clone);
# my $clone_id = $clone->id;
# $clone || $self->throw("Trying to write a clone without a clone object!\n");
# if( !$clone->isa('Bio::EnsEMBL::DB::CloneI') ) {
# $self->throw("Clone '$clone' is not a 'Bio::EnsEMBL::DB::CloneI'");
# }
my @sql;
my $sql = "insert into clone(name, embl_acc, version, embl_version, htg_phase, created, modified) values('$clone_id', '".$clone->embl_id."', ".$clone->version.",".$clone->embl_version.", ".$clone->htg_phase.", FROM_UNIXTIME(".$clone->created."), FROM_UNIXTIME(".$clone->modified."))";
my $sth = $self->prepare($sql);
#my $sth = $self->prepare('insert into clone (clone_id, name, embl_acc, version, embl_version, htg_phase, created, modified) values(?, ?, ?, ?, ?, ?, FROM_UNIXTIME(?), FROM_UNIXTIME(?)');
my $rv = $sth->execute();
# my @sql;
# my $sql = "insert into clone(name, embl_acc, version, embl_version, htg_phase, created, modified) values('$clone_id', '".$clone->embl_id."', ".$clone->version.",".$clone->embl_version.", ".$clone->htg_phase.", FROM_UNIXTIME(".$clone->created."), FROM_UNIXTIME(".$clone->modified."))";
# my $sth = $self->prepare($sql);
# #my $sth = $self->prepare('insert into clone (clone_id, name, embl_acc, version, embl_version, htg_phase, created, modified) values(?, ?, ?, ?, ?, ?, FROM_UNIXTIME(?), FROM_UNIXTIME(?)');
# my $rv = $sth->execute();
$self->throw("Failed to insert clone $clone_id") unless $rv;
$sth = $self->prepare("select last_insert_id()");
my $res = $sth->execute;
my $row = $sth->fetchrow_hashref;
$sth->finish;
my $id = $row->{'last_insert_id()'};
#print(STDERR "Clone $clone_id - $id\n");
# $self->throw("Failed to insert clone $clone_id") unless $rv;
# $sth = $self->prepare("select last_insert_id()");
# my $res = $sth->execute;
# my $row = $sth->fetchrow_hashref;
# $sth->finish;
# my $id = $row->{'last_insert_id()'};
# #print(STDERR "Clone $clone_id - $id\n");
foreach my $contig ( $clone->get_all_Contigs() ) {
$self->write_Contig($contig,$id);
}
# foreach my $contig ( $clone->get_all_Contigs() ) {
# $self->write_Contig($contig,$id);
# }
}
......@@ -588,62 +594,68 @@ sub write_Clone {
sub write_Contig {
my($self, $contig, $clone) = @_;
$self->warn("this method is depreciated please use Bio::EnsEMBL::DBSQL::RawContigAdaptor->store()\n");
my $rca = $self->get_RawContigAdaptor();
$rca->store($contig, $clone);
#Why do we have $clone if contig->cloneid is ok?
$self->throw("$contig is not a Bio::EnsEMBL::DB::ContigI - cannot insert contig for clone $clone")
unless $contig->isa('Bio::EnsEMBL::DB::ContigI');
my $dna = $contig->primary_seq || $self->throw("No sequence in contig object");
$dna->id || $self->throw("No contig id entered.");
$clone || $self->throw("No clone entered.");
# (defined($contig->species) && $contig->species ->isa("Bio::EnsEMBL::Species")) || $self->throw("No species object defined");
# (defined($contig->chromosome) && $contig->chromosome->isa("Bio::EnsEMBL::Chromosome"))
# || $self->throw("No chromosomeobject defined");
# $self->throw("$contig is not a Bio::EnsEMBL::DB::ContigI - cannot insert contig for clone $clone")
# unless $contig->isa('Bio::EnsEMBL::DB::ContigI');
# my $dna = $contig->primary_seq || $self->throw("No sequence in contig object");
# $dna->id || $self->throw("No contig id entered.");
# $clone || $self->throw("No clone entered.");
## (defined($contig->species) && $contig->species ->isa("Bio::EnsEMBL::Species")) || $self->throw("No species object defined");
## (defined($contig->chromosome) && $contig->chromosome->isa("Bio::EnsEMBL::Chromosome"))
## || $self->throw("No chromosomeobject defined");
# my $species_id = $self->write_Species ($contig->species);
# my $chromosome_id = $self->write_Chromosome($contig->chromosome,$species_id);
my $contigid = $contig->id;
my $len = $dna ->length;
my $seqstr = $dna ->seq;
my $offset = $contig->embl_offset();
my $corder = $contig->order();
#my $chromosome_id = $contig->chromosome->get_db_id;
my $international_name = $contig->international_name();
## my $species_id = $self->write_Species ($contig->species);
## my $chromosome_id = $self->write_Chromosome($contig->chromosome,$species_id);
# my $contigid = $contig->id;
# my $len = $dna ->length;
# my $seqstr = $dna ->seq;
# my $offset = $contig->embl_offset();
# my $corder = $contig->order();
# #my $chromosome_id = $contig->chromosome->get_db_id;
# my $international_name = $contig->international_name();
# Insert the sequence into the dna table
$self->_insertSequence($seqstr, $contig->seq_date);
my @sql;
my $sth = $self->prepare("
insert into contig(name, dna_id, length, clone_id, offset, corder, international_name )
values(?, LAST_INSERT_ID(), ?, ?, ?, ?, ?)
");
#print STDERR "contig name = ",$contigid,"\n";
my $rv = $sth->execute(
$contigid,
$len,
$clone,
$offset,
$corder,
$international_name
);
# my @sql;
# my $sth = $self->prepare("
# insert into contig(name, dna_id, length, clone_id, offset, corder, international_name )
# values(?, LAST_INSERT_ID(), ?, ?, ?, ?, ?)
# ");
# #print STDERR "contig name = ",$contigid,"\n";
# my $rv = $sth->execute(
# $contigid,
# $len,
# $clone,
# $offset,
# $corder,
# $international_name
# );
$self->throw("Failed to insert contig $contigid") unless $rv;
# $self->throw("Failed to insert contig $contigid") unless $rv;
$sth = $self->prepare("select last_insert_id()");
$sth->execute;
my ($id) = $sth->fetchrow
or $self->throw("Failed to get last insert id");
#can no longer do this as get_all_SeqFeatures no longer exists
#if a contig is written to the database
# this is a nasty hack. We should have a cleaner way to do this.
#my @features = $contig->get_all_SeqFeatures;
#print(STDERR "Contig $contigid - $id\n");
# write sequence features. We write all of them together as it
# is more efficient
#$self->get_Feature_Obj->write($contig, @features);
# $sth = $self->prepare("select last_insert_id()");
# $sth->execute;
# my ($id) = $sth->fetchrow
# or $self->throw("Failed to get last insert id");
# #can no longer do this as get_all_SeqFeatures no longer exists
# #if a contig is written to the database
# # this is a nasty hack. We should have a cleaner way to do this.
# #my @features = $contig->get_all_SeqFeatures;
# #print(STDERR "Contig $contigid - $id\n");
# # write sequence features. We write all of them together as it
# # is more efficient
# #$self->get_Feature_Obj->write($contig, @features);
return 1;
}
......@@ -665,19 +677,24 @@ sub _insertSequence {
$sequence =~ tr/atgcn/ATGCN/;
$self->warn("this method is depreciated please use Bio::EnsEMBL::RawContigAdaptor->_insertSequence\n");
my $rca = $self->get_RawContigAdaptor();
if ($self->dnadb ne $self) {
$self->throw("ERROR: Trying to write to a remote dna database");
}
$rca->_insertSequence($sequence, $date);
#if ($self->dnadb ne $self) {
# $self->throw("ERROR: Trying to write to a remote dna database");
# }
my $statement = $self->prepare("
insert into dna(sequence,created)
values(?, FROM_UNIXTIME(?))
");
# my $statement = $self->prepare("
# insert into dna(sequence,created)
# values(?, FROM_UNIXTIME(?))
# ");
my $rv = $statement->execute($sequence, $date);
# my $rv = $statement->execute($sequence, $date);
$self->throw("Failed to insert dna $sequence") unless $rv;
# $self->throw("Failed to insert dna $sequence") unless $rv;
}
......
modules/Bio/EnsEMBL/DBSQL/RawContigAdaptor.pm
+ 71
− 0
View file @ 17b6bdff
......@@ -244,5 +244,76 @@ sub _fill_contig_from_arrayref {
}
sub store{
my($self, $contig, $clone_id) = @_;
$self->throw("$contig is not a Bio::EnsEMBL::DB::ContigI - cannot insert contig for clone $clone_id")
unless $contig->isa('Bio::EnsEMBL::DB::ContigI');
my $dna = $contig->primary_seq || $self->throw("No sequence in contig object");
$dna->id || $self->throw("No contig id entered.");
$clone_id || $self->throw("No clone_id entered.");
$self->_insertSequence($dna->seq, $contig->seq_date);
my $sql = "insert into contig(name,
dna_id,
length,
clone_id,
offset,
corder,
international_name)
values('".$contig->id."',
LAST_INSERT_ID(),
".$contig->primary_seq->length." ,
".$clone_id." ,
".$contig->embl_offset." ,
".$contig->order." ,
".$contig->international_name.")";
my $sth = $self->prepare($sql);
my $rv = $sth->execute();
$self->throw("Failed to insert contig ".$contig->id."\n") unless $rv;
$sth = $self->prepare("select last_insert_id()");
$sth->execute;
my ($id) = $sth->fetchrow
or $self->throw("Failed to get last insert id");
#can no longer do this as get_all_SeqFeatures no longer exists
#if a contig is written to the database
# this is a nasty hack. We should have a cleaner way to do this.
#my @features = $contig->get_all_SeqFeatures;
#print(STDERR "Contig $contigid - $id\n");
# write sequence features. We write all of them together as it
# is more efficient
#$self->get_Feature_Obj->write($contig, @features);
return 1;
}
sub _insertSequence{
my ($self, $sequence, $date) = @_;
$sequence =~ tr/atgcn/ATGCN/;
my $statement = $self->prepare("
insert into dna(sequence,created)
values(?, FROM_UNIXTIME(?))
");
my $rv = $statement->execute($sequence, $date);
$self->throw("Failed to insert dna $sequence") unless $rv;
}
1;
modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm
+ 2
− 1
View file @ 17b6bdff
......@@ -6,6 +6,7 @@ package Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::RepeatFeature;
use Bio::LocationI;
use vars qw(@ISA);
@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
......@@ -211,7 +212,7 @@ sub store {
$rf->repeat_id($cons->dbID);
}
}
#print STDERR "repeat = ".$rf->analysis." ".$rf->analysis->dbID."\n";
$sth->execute(
$contig_id,
$rf->start,
......
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