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Commit 0e2e6383 authored by Dan Staines's avatar Dan Staines
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reformatted to use new perltidy options

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modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
+ 142
− 186
View file @ 0e2e6383
=head1 LICENSE
Copyright (c) 1999-2012 The European Bioinformatics Institute and
......@@ -42,7 +43,6 @@ Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor
=cut
package Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor;
use strict;
......@@ -54,7 +54,6 @@ use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_all_by_translation_id
Arg [1] : int $transl
......@@ -75,62 +74,51 @@ use vars qw(@ISA);
=cut
sub fetch_all_by_translation_id {
my($self,$translation_id) = @_;
my ($self, $translation_id) = @_;
if(!$translation_id) {
throw("translation_id argument is required\n");
if (!$translation_id) {
throw("translation_id argument is required\n");
}
my @features;
my $analysis_adaptor = $self->db()->get_AnalysisAdaptor();
my $sth = $self->prepare
("SELECT protein_feature_id, p.seq_start, p.seq_end, p.analysis_id, " .
" p.score, p.perc_ident, p.evalue, p.hit_start, p.hit_end, " .
" p.hit_name, x.display_label, i.interpro_ac " .
"FROM protein_feature p " .
"LEFT JOIN interpro AS i ON p.hit_name = i.id " .
"LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac " .
"WHERE p.translation_id = ?");
$sth->bind_param(1,$translation_id,SQL_INTEGER);
my $sth = $self->prepare("SELECT protein_feature_id, p.seq_start, p.seq_end, p.analysis_id, " . " p.score, p.perc_ident, p.evalue, p.hit_start, p.hit_end, " . " p.hit_name, x.display_label, i.interpro_ac " . "FROM protein_feature p " . "LEFT JOIN interpro AS i ON p.hit_name = i.id " . "LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac " . "WHERE p.translation_id = ?");
$sth->bind_param(1, $translation_id, SQL_INTEGER);
$sth->execute();
while( my $row = $sth->fetchrow_arrayref) {
my ($dbID, $start, $end, $analysisid, $score, $perc_id, $evalue, $hstart,
$hend,$hid,$desc, $interpro_ac) = @$row;
my $analysis = $analysis_adaptor->fetch_by_dbID($analysisid);
if(!$analysis) {
warning("Analysis with dbID=$analysisid does not exist\n" .
"but is referenced by ProteinFeature $dbID");
}
my $feat = Bio::EnsEMBL::ProteinFeature->new
(-DBID => $dbID,
-ADAPTOR => $self,
-SEQNAME => $translation_id,
-START => $start,
-END => $end,
-ANALYSIS => $analysis,
-PERCENT_ID => $perc_id,
-P_VALUE => $evalue,
-SCORE => $score,
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hid,
-IDESC => $desc,
-INTERPRO_AC => $interpro_ac);
push(@features,$feat);
}
while (my $row = $sth->fetchrow_arrayref) {
my ($dbID, $start, $end, $analysisid, $score, $perc_id, $evalue, $hstart, $hend, $hid, $desc, $interpro_ac) = @$row;
my $analysis = $analysis_adaptor->fetch_by_dbID($analysisid);
if (!$analysis) {
warning("Analysis with dbID=$analysisid does not exist\n" . "but is referenced by ProteinFeature $dbID");
}
my $feat = Bio::EnsEMBL::ProteinFeature->new(-DBID => $dbID,
-ADAPTOR => $self,
-SEQNAME => $translation_id,
-START => $start,
-END => $end,
-ANALYSIS => $analysis,
-PERCENT_ID => $perc_id,
-P_VALUE => $evalue,
-SCORE => $score,
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hid,
-IDESC => $desc,
-INTERPRO_AC => $interpro_ac);
push(@features, $feat);
} ## end while (my $row = $sth->fetchrow_arrayref)
$sth->finish();
return \@features;
}
return \@features;
} ## end sub fetch_all_by_translation_id
=head2 fetch_by_dbID
......@@ -145,52 +133,40 @@ sub fetch_all_by_translation_id {
=cut
sub fetch_by_dbID{
my ($self,$protfeat_id) = @_;
my $sth = $self->prepare(
"SELECT p.seq_start, p.seq_end, p.analysis_id, " .
" p.score, p.perc_ident, p.evalue, " .
" p.hit_start, p.hit_end, p.hit_name, " .
" x.display_label, i.interpro_ac " .
"FROM protein_feature p " .
"LEFT JOIN interpro AS i ON p.hit_name = i.id " .
"LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac " .
"WHERE p.protein_feature_id = ?");
$sth->bind_param(1,$protfeat_id,SQL_INTEGER);
sub fetch_by_dbID {
my ($self, $protfeat_id) = @_;
my $sth = $self->prepare("SELECT p.seq_start, p.seq_end, p.analysis_id, " . " p.score, p.perc_ident, p.evalue, " . " p.hit_start, p.hit_end, p.hit_name, " . " x.display_label, i.interpro_ac " . "FROM protein_feature p " . "LEFT JOIN interpro AS i ON p.hit_name = i.id " . "LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac " . "WHERE p.protein_feature_id = ?");
$sth->bind_param(1, $protfeat_id, SQL_INTEGER);
my $res = $sth->execute();
if($sth->rows == 0) {
$sth->finish();
return undef;
if ($sth->rows == 0) {
$sth->finish();
return undef;
}
my ($start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart,
$hend, $hseqname, $idesc, $interpro_ac) = $sth->fetchrow_array();
my ($start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart, $hend, $hseqname, $idesc, $interpro_ac) = $sth->fetchrow_array();
$sth->finish();
my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
return Bio::EnsEMBL::ProteinFeature->new
(-ADAPTOR => $self,
-DBID => $protfeat_id,
-START => $start,
-END => $end,
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hseqname,
-ANALYSIS => $analysis,
-SCORE => $score,
-P_VALUE => $pvalue,
-PERCENT_ID => $perc_ident,
-IDESC => $idesc,
-INTERPRO_AC => $interpro_ac);
}
return
Bio::EnsEMBL::ProteinFeature->new(-ADAPTOR => $self,
-DBID => $protfeat_id,
-START => $start,
-END => $end,
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hseqname,
-ANALYSIS => $analysis,
-SCORE => $score,
-P_VALUE => $pvalue,
-PERCENT_ID => $perc_ident,
-IDESC => $idesc,
-INTERPRO_AC => $interpro_ac);
} ## end sub fetch_by_dbID
=head2 store
......@@ -208,73 +184,56 @@ sub fetch_by_dbID{
=cut
sub store {
my ($self,$feature, $translation_id) = @_;
my ($self, $feature, $translation_id) = @_;
if(!ref($feature) || !$feature->isa('Bio::EnsEMBL::ProteinFeature')) {
throw("ProteinFeature argument is required");
if (!ref($feature) || !$feature->isa('Bio::EnsEMBL::ProteinFeature')) {
throw("ProteinFeature argument is required");
}
if(!$translation_id) {
deprecate("Calling ProteinFeatureAdaptor without a translation_id is " .
"deprecated. Pass a translation_id argument rather than " .
"setting the ProteinFeature seqname to be the translation " .
"id");
$translation_id = $feature->seqname();
if (!$translation_id) {
deprecate("Calling ProteinFeatureAdaptor without a translation_id is " . "deprecated. Pass a translation_id argument rather than " . "setting the ProteinFeature seqname to be the translation " . "id");
$translation_id = $feature->seqname();
}
my $db = $self->db();
if($feature->is_stored($db)) {
warning("ProteinFeature " . $feature->dbID() . " is already stored in " .
"this database - not storing again");
if ($feature->is_stored($db)) {
warning("ProteinFeature " . $feature->dbID() . " is already stored in " . "this database - not storing again");
}
my $analysis = $feature->analysis();
if (!defined($analysis)) {
throw("Feature doesn't have analysis. Can't write to database");
throw("Feature doesn't have analysis. Can't write to database");
}
if(!$analysis->is_stored($db)) {
$db->get_AnalysisAdaptor->store($analysis);
if (!$analysis->is_stored($db)) {
$db->get_AnalysisAdaptor->store($analysis);
}
my $sth =
$self->prepare("INSERT INTO protein_feature " .
" SET translation_id = ?, " .
" seq_start = ?, ".
" seq_end = ?, ".
" analysis_id = ?, ".
" hit_start = ?, ".
" hit_end = ?, ".
" hit_name = ?, ".
" score = ?, ".
" perc_ident = ?, ".
" evalue = ?");
$sth->bind_param(1,$translation_id,SQL_INTEGER);
$sth->bind_param(2,$feature->start,SQL_INTEGER);
$sth->bind_param(3,$feature->end,SQL_INTEGER);
$sth->bind_param(4,$analysis->dbID,SQL_INTEGER);
$sth->bind_param(5,$feature->hstart,SQL_INTEGER);
$sth->bind_param(6,$feature->hend,SQL_INTEGER);
$sth->bind_param(7,$feature->hseqname,SQL_VARCHAR);
$sth->bind_param(8,$feature->score,SQL_DOUBLE);
$sth->bind_param(9,$feature->percent_id,SQL_FLOAT);
$sth->bind_param(10,$feature->p_value,SQL_DOUBLE);
my $sth = $self->prepare("INSERT INTO protein_feature " . " SET translation_id = ?, " . " seq_start = ?, " . " seq_end = ?, " . " analysis_id = ?, " . " hit_start = ?, " . " hit_end = ?, " . " hit_name = ?, " . " score = ?, " . " perc_ident = ?, " . " evalue = ?");
$sth->bind_param(1, $translation_id, SQL_INTEGER);
$sth->bind_param(2, $feature->start, SQL_INTEGER);
$sth->bind_param(3, $feature->end, SQL_INTEGER);
$sth->bind_param(4, $analysis->dbID, SQL_INTEGER);
$sth->bind_param(5, $feature->hstart, SQL_INTEGER);
$sth->bind_param(6, $feature->hend, SQL_INTEGER);
$sth->bind_param(7, $feature->hseqname, SQL_VARCHAR);
$sth->bind_param(8, $feature->score, SQL_DOUBLE);
$sth->bind_param(9, $feature->percent_id, SQL_FLOAT);
$sth->bind_param(10, $feature->p_value, SQL_DOUBLE);
$sth->execute();
my $dbID = $sth->{'mysql_insertid'};
$feature->adaptor($self);
$feature->dbID($dbID);
$sth->finish();
return $dbID;
}
$sth->finish();
return $dbID;
} ## end sub store
sub fetch_by_translation_id {
deprecate("Use fetch_all_by_translation_id instead.");
......@@ -282,8 +241,8 @@ sub fetch_by_translation_id {
}
sub fetch_all_by_feature_and_dbID {
my $self = shift;
my $feature = shift;
my $self = shift;
my $feature = shift;
my $translation_id = shift;
deprecate("Use fetch_all_by_translation_id instead.");
......@@ -293,79 +252,76 @@ sub fetch_all_by_feature_and_dbID {
my @out;
foreach my $f (@$features) {
my $logic_name = lc($f->analysis->logic_name());
print STDERR "LOGIC_NAME = $logic_name | FEATURE = $feature\n";
push(@out, $f) if($logic_name eq lc($feature));
my $logic_name = lc($f->analysis->logic_name());
print STDERR "LOGIC_NAME = $logic_name | FEATURE = $feature\n";
push(@out, $f) if ($logic_name eq lc($feature));
}
return \@out;
}
sub save {
my ($self, $features) = @_;
my @feats = @$features;
throw("Must call save with features") if( scalar(@feats) == 0 );
throw("Must call save with features") if (scalar(@feats) == 0);
# my @tabs = $self->_tables;
# my ($tablename) = @{$tabs[0]};
# my @tabs = $self->_tables;
# my ($tablename) = @{$tabs[0]};
my $tablename = 'protein_feature';
my $db = $self->db();
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
my $sql = qq{INSERT INTO $tablename (translation_id, seq_start, seq_end, hit_start, hit_end, hit_name, analysis_id, score, evalue, perc_ident, external_data) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)};
my $sth = $self->prepare($sql);
foreach my $feat ( @feats ) {
if( !ref $feat || !$feat->isa("Bio::EnsEMBL::ProteinFeature") ) {
throw("feature must be a Bio::EnsEMBL::ProteinFeature,". " not a [".ref($feat)."].");
}
if($feat->is_stored($db)) {
warning("ProteinFeature [".$feat->dbID."] is already stored" .
" in this database.");
next;
}
my $hstart = defined $feat->hstart ? $feat->hstart : $feat->start ;
my $hend = defined $feat->hend ? $feat->hend : $feat->end;
if(!defined($feat->analysis)) {
throw("An analysis must be attached to the features to be stored.");
}
#store the analysis if it has not been stored yet
if(!$feat->analysis->is_stored($db)) {
$analysis_adaptor->store($feat->analysis());
}
my $original = $feat;
my $extra_data = $feat->extra_data ? $self->dump_data($feat->extra_data) : '';
$sth->bind_param(1,$feat->translation_id,SQL_INTEGER);
$sth->bind_param(2,$feat->start,SQL_INTEGER);
$sth->bind_param(3,$feat->end,SQL_INTEGER);
$sth->bind_param(4,$hstart,SQL_INTEGER);
$sth->bind_param(5,$hend,SQL_INTEGER);
$sth->bind_param(6,$feat->hseqname,SQL_VARCHAR);
$sth->bind_param(7,$feat->analysis->dbID,SQL_INTEGER);
$sth->bind_param(8,$feat->score,SQL_DOUBLE);
$sth->bind_param(9,$feat->p_value,SQL_DOUBLE);
$sth->bind_param(10,$feat->percent_id,SQL_FLOAT);
$sth->bind_param(11,$extra_data,SQL_LONGVARCHAR);
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
$original->adaptor($self);
}
$sth->finish();
}
foreach my $feat (@feats) {
if (!ref $feat || !$feat->isa("Bio::EnsEMBL::ProteinFeature")) {
throw("feature must be a Bio::EnsEMBL::ProteinFeature," . " not a [" . ref($feat) . "].");
}
if ($feat->is_stored($db)) {
warning("ProteinFeature [" . $feat->dbID . "] is already stored" . " in this database.");
next;
}
my $hstart = defined $feat->hstart ? $feat->hstart : $feat->start;
my $hend = defined $feat->hend ? $feat->hend : $feat->end;
if (!defined($feat->analysis)) {
throw("An analysis must be attached to the features to be stored.");
}
#store the analysis if it has not been stored yet
if (!$feat->analysis->is_stored($db)) {
$analysis_adaptor->store($feat->analysis());
}
my $original = $feat;
my $extra_data = $feat->extra_data ? $self->dump_data($feat->extra_data) : '';
$sth->bind_param(1, $feat->translation_id, SQL_INTEGER);
$sth->bind_param(2, $feat->start, SQL_INTEGER);
$sth->bind_param(3, $feat->end, SQL_INTEGER);
$sth->bind_param(4, $hstart, SQL_INTEGER);
$sth->bind_param(5, $hend, SQL_INTEGER);
$sth->bind_param(6, $feat->hseqname, SQL_VARCHAR);
$sth->bind_param(7, $feat->analysis->dbID, SQL_INTEGER);
$sth->bind_param(8, $feat->score, SQL_DOUBLE);
$sth->bind_param(9, $feat->p_value, SQL_DOUBLE);
$sth->bind_param(10, $feat->percent_id, SQL_FLOAT);
$sth->bind_param(11, $extra_data, SQL_LONGVARCHAR);
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
$original->adaptor($self);
} ## end foreach my $feat (@feats)
$sth->finish();
} ## end sub save
1;
modules/Bio/EnsEMBL/FeaturePair.pm
+ 220
− 271
View file @ 0e2e6383
This diff is collapsed.
modules/Bio/EnsEMBL/ProteinFeature.pm
+ 6
− 15
View file @ 0e2e6383
=head1 LICENSE
Copyright (c) 1999-2012 The European Bioinformatics Institute and
......@@ -15,7 +16,6 @@
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
......@@ -51,8 +51,6 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::FeaturePair);
=head2 new
Arg [IDESC] : (optional) string An interpro description
......@@ -79,8 +77,7 @@ sub new {
my $class = ref($proto) || $proto;
my ( $idesc, $interpro_ac, $translation_id ) =
rearrange( [ 'IDESC', 'INTERPRO_AC', 'TRANSLATION_ID' ], @_ );
my ($idesc, $interpro_ac, $translation_id) = rearrange(['IDESC', 'INTERPRO_AC', 'TRANSLATION_ID'], @_);
my $self = $class->SUPER::new(@_);
......@@ -93,7 +90,6 @@ sub new {
return $self;
}
=head2 strand
Arg [1] : Ignored
......@@ -110,8 +106,6 @@ sub strand {
return $self->{'strand'};
}
=head2 idesc
Arg [1] : (optional) string The interpro description
......@@ -125,14 +119,12 @@ sub strand {
=cut
sub idesc{
sub idesc {
my $self = shift;
$self->{'idesc'} = shift if(@_);
$self->{'idesc'} = shift if (@_);
return $self->{'idesc'};
}
=head2 interpro_ac
Arg [1] : (optional) string The interpro accession
......@@ -146,13 +138,12 @@ sub idesc{
=cut
sub interpro_ac{
sub interpro_ac {
my $self = shift;
$self->{'interpro_ac'} = shift if(@_);
$self->{'interpro_ac'} = shift if (@_);
return $self->{'interpro_ac'};
}
=head2 translation_id
Arg [1] : (optional) integer The dbID of the translation
......
modules/t/proteinFeature.t
+ 34
− 42
View file @ 0e2e6383
use strict;
use warnings;
BEGIN { $| = 1;
use Test;
plan tests => 17;
BEGIN {
$| = 1;
use Test;
plan tests => 17;
}
use Bio::EnsEMBL::Test::TestUtils;
......@@ -12,46 +12,41 @@ use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::ProteinFeature;
use Bio::EnsEMBL::Analysis;
our $verbose = 0; #turn on or off debug statements
our $verbose = 0; #turn on or off debug statements
#
# Test new and getters
#
my $start = 10;
my $end = 100;
my $hstart = 1;
my $hend = 90;
my $hstrand = 1;
my $hseqname = 'RF1231';
my $start = 10;
my $end = 100;
my $hstart = 1;
my $hend = 90;
my $hstrand = 1;
my $hseqname = 'RF1231';
my $percent_id = 90.8;
my $p_value = '1.52';
my $score = 50;
my $species = 'Homo_sapiens';
my $hspecies = 'Mus_musculus';
my $p_value = '1.52';
my $score = 50;
my $species = 'Homo_sapiens';
my $hspecies = 'Mus_musculus';
my $idesc = 'interpro description';
my $idesc = 'interpro description';
my $interpro_ac = 'interpro accession';
my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
my $f = Bio::EnsEMBL::ProteinFeature->new
(-START => $start,
-END => $end,
-ANALYSIS => $analysis,
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hseqname,
-PERCENT_ID => $percent_id,
-P_VALUE => $p_value,
-SCORE => $score,
-SPECIES => $species,
-HSPECIES => $hspecies,
-IDESC => $idesc,
-INTERPRO_AC => $interpro_ac);
my $f = Bio::EnsEMBL::ProteinFeature->new(-START => $start,
-END => $end,
-ANALYSIS => $analysis,
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hseqname,
-PERCENT_ID => $percent_id,
-P_VALUE => $p_value,
-SCORE => $score,
-SPECIES => $species,
-HSPECIES => $hspecies,
-IDESC => $idesc,
-INTERPRO_AC => $interpro_ac);
ok($f && $f->isa('Bio::EnsEMBL::ProteinFeature'));
......@@ -60,15 +55,15 @@ ok($f->end == $end);
ok($f->analysis == $analysis);
ok($f->hstart == $hstart);
ok($f->hend == $hend);
ok($f->hend == $hend);
ok($f->hseqname eq $hseqname);
ok($f->percent_id == $percent_id);
ok($f->p_value == $p_value);
ok($f->score == $score);
ok($f->species eq $species);
ok($f->species eq $species);
ok($f->hspecies eq $hspecies);
ok($f->idesc eq $idesc);
ok($f->idesc eq $idesc);
ok($f->interpro_ac eq $interpro_ac);
# check that the strand is 0
......@@ -77,9 +72,6 @@ ok($f->strand == 0);
#
# Test setters
#
ok(test_getter_setter($f, 'idesc', 'interpro desc1'));
ok(test_getter_setter($f, 'interpro_ac', 'interpro ac1'));
ok(test_getter_setter($f, 'idesc', 'interpro desc1'));
ok(test_getter_setter($f, 'interpro_ac', 'interpro ac1'));
modules/t/proteinFeatureAdaptor.t
+ 7
− 9
View file @ 0e2e6383
......@@ -2,9 +2,10 @@ use strict;
use Bio::EnsEMBL::Test::TestUtils;
BEGIN { $| = 1;
use Test;
plan tests => 2;
BEGIN {
$| = 1;
use Test;
plan tests => 2;
}
use Bio::EnsEMBL::Test::MultiTestDB;
......@@ -16,7 +17,6 @@ my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
# get a core DBAdaptor
my $dba = $multi->get_DBAdaptor("core");
#
# Test get_ProteinFeatureAdaptor works
#
......@@ -24,7 +24,6 @@ my $pfa = $dba->get_ProteinFeatureAdaptor();
ok($pfa && ref($pfa) && $pfa->isa('Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor'));
my $pfs = $pfa->fetch_all_by_translation_id(21724);
print_features($pfs);
......@@ -34,9 +33,8 @@ ok(@$pfs == 15);
sub print_features {
my $features = shift;
foreach my $f (@$features) {
if(defined($f)) {
debug($f->start.'-'.$f->end. ' -> '.$f->hseqname. ':'.
$f->hstart. '-'.$f->hend);
}
if (defined($f)) {
debug($f->start . '-' . $f->end . ' -> ' . $f->hseqname . ':' . $f->hstart . '-' . $f->hend);
}
}
}
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