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Commit da06bc0a authored by Laura Clarke's avatar Laura Clarke
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All contain a variety of bug fixes, ProteinAlignFeatureAdaptor has been... 

All contain a variety of bug fixes, ProteinAlignFeatureAdaptor  has been altered to return DnaPepAlignFeatures
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modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
+ 40
− 31
View file @ da06bc0a
......@@ -81,10 +81,10 @@ sub fetch_by_dbID{
$self->throw("fetch_by_dbID must have an id");
}
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line,p.analysis_id from dna_align_feature p where p.dna_align_feature_id = $id");
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line,p.analysis_id, p.score from dna_align_feature p where p.dna_align_feature_id = $id");
$sth->execute();
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hstrand,$hname,$cigar,$analysis_id) = $sth->fetchrow_array();
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hstrand,$hname,$cigar,$analysis_id, $score) = $sth->fetchrow_array();
if( !defined $contig_id ) {
$self->throw("No simple feature with id $id");
......@@ -96,7 +96,7 @@ sub fetch_by_dbID{
$out->start($start);
$out->end($end);
$out->strand($strand);
$out->score($score);
$out->hstart($hstart);
$out->hend($hend);
$out->hstrand($hstrand);
......@@ -148,7 +148,7 @@ sub fetch_by_contig_id{
}
my $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();
my $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();;
$out->start($start);
$out->end($end);
$out->strand($strand);
......@@ -180,12 +180,12 @@ sub fetch_by_contig_id_and_logic_name{
$self->throw("must provide a logic_name to fetch by logic name: $!\n");
}
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_name, p.cigar_line,p.analysis_id from dna_align_feature p, analysis a where p.contig_id = $cid and a.analysis_id = p.analysis_id and a.logic_name = '$logic_name'");
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_name, p.cigar_line,p.analysis_id, p.score from dna_align_feature p, analysis a where p.contig_id = $cid and a.analysis_id = p.analysis_id and a.logic_name = '$logic_name'");
$sth->execute();
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hname, $cigar,$analysis_id);
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hname, $cigar,$analysis_id, $score);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id, \$score);
my @f;
my $contig = $self->db->get_RawContigAdaptor->fetch_by_dbID($cid);
......@@ -201,7 +201,7 @@ sub fetch_by_contig_id_and_logic_name{
$out->start($start);
$out->end($end);
$out->strand($strand);
$out->score($score);
$out->hstart($hstart);
$out->hend($hend);
$out->hseqname($hname);
......@@ -241,12 +241,12 @@ sub fetch_by_contig_id_and_dbname{
push(@analysis_ids, $analysis_id);
}
my $analysis_idlist = join(',', @analysis_ids);
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_name, p.cigar_line,p.analysis_id from dna_align_feature p where p.contig_id = $cid and p.analysis_id in($analysis_idlist)");
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_name, p.cigar_line,p.analysis_id, p.score from dna_align_feature p where p.contig_id = $cid and p.analysis_id in($analysis_idlist)");
$sth->execute();
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hname, $cigar,$analysis_id);
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hname, $cigar,$analysis_id, $score);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id, \$score);
my @f;
my $contig = $self->db->get_RawContigAdaptor->fetch_by_dbID($cid);
......@@ -262,7 +262,7 @@ sub fetch_by_contig_id_and_dbname{
$out->start($start);
$out->end($end);
$out->strand($strand);
$out->score($score);
$out->hstart($hstart);
$out->hend($hend);
$out->hseqname($hname);
......@@ -312,15 +312,15 @@ sub fetch_by_assembly_location{
# build the SQL
print STDERR "have @cids contig ids\n";
my $cid_list = join(',',@cids);
my $sql = "select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line,a.gff_source,a.gff_feature from dna_align_feature p where p.contig_id in ($cid_list)";
my $sql = "select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line, p.score from dna_align_feature p where p.contig_id in ($cid_list)";
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line, p.analysis_id from dna_align_feature p where p.contig_id in ($cid_list)");
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line, p.analysis_id, p.score from dna_align_feature p where p.contig_id in ($cid_list)");
$sth->execute();
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hstrand,$hname,$cigar,$analysis_id);
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hstrand,$hname,$cigar,$analysis_id, $score);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hstrand, \$hname,\$cigar,\$analysis_id);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hstrand, \$hname,\$cigar,\$analysis_id. \$score);
my @f;
......@@ -354,7 +354,7 @@ sub fetch_by_assembly_location{
$out->end($coord_list[0]->end);
$out->strand($coord_list[0]->strand);
$out->seqname($coord_list[0]->id);
$out->score($score);
$out->hstart($hstart);
$out->hend($hend);
$out->hstrand($hstrand);
......@@ -408,14 +408,14 @@ sub fetch_by_assembly_location_and_dbname{
push(@analysis_ids, $analysis_id);
}
my $analysis_idlist = join(',', @analysis_ids);
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_name, p.cigar_line,p.analysis_id from dna_align_feature p where p.contig_id in($cid_list) and a.analysis_id = p.analysis_id and p.analysis_id in($analysis_idlist)");
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_name, p.cigar_line,p.analysis_id, p.score from dna_align_feature p where p.contig_id in($cid_list) and a.analysis_id = p.analysis_id and p.analysis_id in($analysis_idlist)");
$sth->execute();
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hname, $cigar,$analysis_id);
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hname, $cigar,$analysis_id, $score);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id, \$score);
my @f;
my @f;
my %ana;
while( $sth->fetch ) {
......@@ -432,13 +432,17 @@ sub fetch_by_assembly_location_and_dbname{
}
# ok, ready to build a sequence feature: do we want this relative or not?
if($coord_list[0]->isa("Bio::EnsEMBL::Mapper::Gap")){
#print STDERR "the gap is from ".$coord_list[0]->start." to ".$coord_list[0]->end." on contig ".$contig_id."\n";
$self->warn("feature is on a piece of contig not on golden path or in a gap skipping as not needed\n");
next;
}
my $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();;
$out->start($coord_list[0]->start);
$out->end($coord_list[0]->end);
$out->strand($coord_list[0]->strand);
$out->seqname($coord_list[0]->seqname);
$out->score($score);
$out->hstart($hstart);
$out->hend($hend);
$out->hseqname($hname);
......@@ -478,12 +482,12 @@ sub fetch_by_assembly_location_and_logic_name{
my $cid_list = join(',',@cids);
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_name, p.cigar_line,p.analysis_id from dna_align_feature p, analysis a where p.contig_id in($cid_list) and a.analysis_id = p.analysis_id and a.logic_name = '$logic_name'");
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_name, p.cigar_line,p.analysis_id, p.score from dna_align_feature p, analysis a where p.contig_id in($cid_list) and a.analysis_id = p.analysis_id and a.logic_name = '$logic_name'");
$sth->execute();
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hname, $cigar,$analysis_id);
my ($contig_id,$start,$end,$strand,$hstart,$hend,$hname, $cigar,$analysis_id, $score);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id);
$sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id, \$score);
my @f;
......@@ -501,7 +505,12 @@ sub fetch_by_assembly_location_and_logic_name{
if( !defined $ana{$analysis_id} ) {
$ana{$analysis_id} = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
}
if($coord_list[0]->isa("Bio::EnsEMBL::Mapper::Gap")){
#print STDERR "the gap is from ".$coord_list[0]->start." to ".$coord_list[0]->end." on contig ".$contig_id."\n";
$self->warn("feature is on a piece of contig not on golden path or in a gap skipping as not needed\n");
next;
}
# ok, ready to build a sequence feature: do we want this relative or not?
my $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();;
......@@ -509,7 +518,7 @@ sub fetch_by_assembly_location_and_logic_name{
$out->end($coord_list[0]->end);
$out->strand($coord_list[0]->strand);
$out->seqname($coord_list[0]->seqname);
$out->score($score);
$out->hstart($hstart);
$out->hend($hend);
$out->hseqname($hname);
......@@ -546,7 +555,7 @@ sub store{
$self->throw("Contig_id must be a number, not [$contig_id]");
}
my $sth = $self->prepare("insert into dna_align_feature (contig_id,contig_start,contig_end,contig_strand,hit_start,hit_end,hit_strand,hit_name,cigar_line,analysis_id,score) values (?,?,?,?,?,?,?,?,?,?,?)");
my $sth = $self->prepare("insert into dna_align_feature (contig_id,contig_start,contig_end,contig_strand,hit_start,hit_end,hit_strand,hit_name,cigar_line,analysis_id,score,evalue, perc_ident) values (?,?,?,?,?,?,?,?,?,?,?, ?, ?)");
foreach my $sf ( @sf ) {
if( !ref $sf || !$sf->isa("Bio::EnsEMBL::FeaturePair") ) {
......@@ -560,8 +569,8 @@ sub store{
# maybe we should throw here. Shouldn't we always have an analysis from the database?
$self->throw("I think we should always have an analysis object which has originated from the database. No dbID, not putting in!");
}
$sth->execute($contig_id,$sf->start,$sf->end,$sf->strand,$sf->hstart,$sf->hend,$sf->hstrand,$sf->hseqname,$sf->cigar_string,$sf->analysis->dbID,$sf->score);
print STDERR "storing ".$sf->gffstring."\n";
$sth->execute($contig_id,$sf->start,$sf->end,$sf->strand,$sf->hstart,$sf->hend,$sf->hstrand,$sf->hseqname,$sf->cigar_string,$sf->analysis->dbID,$sf->score, $sf->p_value, $sf->percent_id);
}
......
modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
+ 235
− 383
View file @ da06bc0a
This diff is collapsed.
modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
+ 15
− 9
View file @ da06bc0a
......@@ -196,15 +196,16 @@ sub fetch_by_assembly_location_and_logic_name{
}
my $mapper = $self->db->get_AssemblyMapperAdaptor->fetch_by_type($type);
$mapper->register_region($start,$end,$chr);
$mapper->register_region($chr,$start,$end);
my @cids = $mapper->list_contig_ids($start,$end,$chr);
print
my @cids = $mapper->list_contig_ids($chr,$start,$end);
print "have ".scalar(@cids)." contig ids\n";
# build the SQL
my $cid_list = join(', ',@cids);
print $cid_list."\n";
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.analysis_id, p.score from protein_align_feature p, analysis a where p.contig_id in ($cid_list) and a.analysis_id = p.analysis_id and a.logic_name = '$logic_name'");
print "select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.analysis_id, p.score from simple_feature p, analysis a where p.contig_id in (".$cid_list.") and a.analysis_id = p.analysis_id and a.logic_name = '".$logic_name."'\n";
my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.analysis_id, p.score from simple_feature p, analysis a where p.contig_id in ($cid_list) and a.analysis_id = p.analysis_id and a.logic_name = '$logic_name'");
$sth->execute();
my ($contig_id,$start,$end,$strand,$display,$analysis_id);
......@@ -215,7 +216,7 @@ sub fetch_by_assembly_location_and_logic_name{
while( $sth->fetch ) {
# we whether this is sensible to use or not
my @coord_list = $mapper->map_coordinates_to_assembly($start,$end,$strand,$contig_id);
my @coord_list = $mapper->map_coordinates_to_assembly($contig_id, $start,$end,$strand);
# coord list > 1 - means does not cleanly map. At the moment, skip
if( scalar(@coord_list) > 1 ) {
......@@ -267,9 +268,9 @@ sub fetch_by_assembly_location{
}
my $mapper = $self->db->get_AssemblyMapperAdaptor->fetch_by_type($type);
$mapper->register_region($start,$end,$chr);
$mapper->register_region($chr, $start,$end);
my @cids = $mapper->list_contig_ids($start,$end,$chr);
my @cids = $mapper->list_contig_ids($chr, $start,$end);
# build the SQL
......@@ -285,7 +286,7 @@ sub fetch_by_assembly_location{
while( $sth->fetch ) {
# we whether this is sensible to use or not
my @coord_list = $mapper->map_coordinates_to_assembly($start,$end,$strand,$contig_id);
my @coord_list = $mapper->map_coordinates_to_assembly($contig_id, $start,$end,$strand);
# coord list > 1 - means does not cleanly map. At the moment, skip
if( scalar(@coord_list) > 1 ) {
......@@ -295,7 +296,12 @@ sub fetch_by_assembly_location{
if( !defined $ana{$analysis_id} ) {
$ana{$analysis_id} = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
}
if($coord_list[0]->isa("Bio::EnsEMBL::Mapper::Gap")){
#print STDERR "the gap is from ".$coord_list[0]->start." to ".$coord_list[0]->end." on contig ".$contig_id."\n";
$self->warn("feature is on a piece of contig not on golden path or in a gap skipping as not needed\n");
#$counter++;
next;
}
# ok, ready to build a sequence feature: do we want this relative or not?
my $out = Bio::EnsEMBL::SimpleFeature->new();
......
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