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Commit eacfb265 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Handle cicular chromosomes in _objs_from_sth(). Patch from EG.

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modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+ 151
− 81
View file @ eacfb265
...@@ -515,7 +515,7 @@ sub list_stable_ids { ...@@ -515,7 +515,7 @@ sub list_stable_ids {
# Caller : internal # Caller : internal
sub _objs_from_sth { sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_; my ( $self, $sth, $mapper, $dest_slice ) = @_;
# #
# This code is ugly because an attempt has been made to remove as many # This code is ugly because an attempt has been made to remove as many
...@@ -530,21 +530,17 @@ sub _objs_from_sth { ...@@ -530,21 +530,17 @@ sub _objs_from_sth {
my %sr_name_hash; my %sr_name_hash;
my %sr_cs_hash; my %sr_cs_hash;
my ( my ( $exon_id, $seq_region_id, $seq_region_start,
$exon_id, $seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $phase,
$seq_region_end, $seq_region_strand, $phase, $end_phase, $is_current, $is_constitutive,
$end_phase, $is_current, $is_constitutive, $stable_id, $version, $created_date,
$stable_id, $version, $created_date, $modified_date );
$modified_date
);
$sth->bind_columns( $sth->bind_columns( \( $exon_id, $seq_region_id, $seq_region_start,
\$exon_id, \$seq_region_id, \$seq_region_start, $seq_region_end, $seq_region_strand, $phase,
\$seq_region_end, \$seq_region_strand, \$phase, $end_phase, $is_current, $is_constitutive,
\$end_phase, \$is_current, \$is_constitutive, $stable_id, $version, $created_date,
\$stable_id, \$version, \$created_date, $modified_date ) );
\$modified_date
);
my $asm_cs; my $asm_cs;
my $cmp_cs; my $cmp_cs;
...@@ -552,9 +548,10 @@ sub _objs_from_sth { ...@@ -552,9 +548,10 @@ sub _objs_from_sth {
my $asm_cs_name; my $asm_cs_name;
my $cmp_cs_vers; my $cmp_cs_vers;
my $cmp_cs_name; my $cmp_cs_name;
if($mapper) {
$asm_cs = $mapper->assembled_CoordSystem(); if ($mapper) {
$cmp_cs = $mapper->component_CoordSystem(); $asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name(); $asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version(); $asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name(); $cmp_cs_name = $cmp_cs->name();
...@@ -569,38 +566,42 @@ sub _objs_from_sth { ...@@ -569,38 +566,42 @@ sub _objs_from_sth {
my $dest_slice_sr_name; my $dest_slice_sr_name;
my $dest_slice_sr_id; my $dest_slice_sr_id;
my $asma; my $asma;
if($dest_slice) {
$dest_slice_start = $dest_slice->start(); if ($dest_slice) {
$dest_slice_end = $dest_slice->end(); $dest_slice_start = $dest_slice->start();
$dest_slice_strand = $dest_slice->strand(); $dest_slice_end = $dest_slice->end();
$dest_slice_length = $dest_slice->length(); $dest_slice_strand = $dest_slice->strand();
$dest_slice_cs = $dest_slice->coord_system(); $dest_slice_length = $dest_slice->length();
$dest_slice_cs = $dest_slice->coord_system();
$dest_slice_sr_name = $dest_slice->seq_region_name(); $dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id(); $dest_slice_sr_id = $dest_slice->get_seq_region_id();
$asma = $self->db->get_AssemblyMapperAdaptor(); $asma = $self->db->get_AssemblyMapperAdaptor();
} }
FEATURE: while($sth->fetch()) { FEATURE: while ( $sth->fetch() ) {
#need to get the internal_seq_region, if present #need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id); $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
my $slice = $slice_hash{"ID:".$seq_region_id}; my $slice = $slice_hash{ "ID:" . $seq_region_id };
my $dest_mapper = $mapper; my $dest_mapper = $mapper;
if(!$slice) { if ( !$slice ) {
$slice = $sa->fetch_by_seq_region_id($seq_region_id); $slice = $sa->fetch_by_seq_region_id($seq_region_id);
$slice_hash{"ID:".$seq_region_id} = $slice; $slice_hash{ "ID:" . $seq_region_id } = $slice;
$sr_name_hash{$seq_region_id} = $slice->seq_region_name(); $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
$sr_cs_hash{$seq_region_id} = $slice->coord_system(); $sr_cs_hash{$seq_region_id} = $slice->coord_system();
} }
#obtain a mapper if none was defined, but a dest_seq_region was #obtain a mapper if none was defined, but a dest_seq_region was
if(!$dest_mapper && $dest_slice && if ( !$dest_mapper
!$dest_slice_cs->equals($slice->coord_system)) { && $dest_slice
$dest_mapper = $asma->fetch_by_CoordSystems($dest_slice_cs, && !$dest_slice_cs->equals( $slice->coord_system ) )
$slice->coord_system); {
$asm_cs = $dest_mapper->assembled_CoordSystem(); $dest_mapper =
$cmp_cs = $dest_mapper->component_CoordSystem(); $asma->fetch_by_CoordSystems( $dest_slice_cs,
$slice->coord_system );
$asm_cs = $dest_mapper->assembled_CoordSystem();
$cmp_cs = $dest_mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name(); $asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version(); $asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name(); $cmp_cs_name = $cmp_cs->name();
...@@ -630,57 +631,126 @@ sub _objs_from_sth { ...@@ -630,57 +631,126 @@ sub _objs_from_sth {
} }
# #
# If a destination slice was provided convert the coords # If a destination slice was provided convert the coords. If the
# If the dest_slice starts at 1 and is foward strand, nothing needs doing # dest_slice starts at 1 and is foward strand, nothing needs doing.
# #
if($dest_slice) { if ( defined($dest_slice) ) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) { if ( $dest_slice_strand == 1 ) {
if($dest_slice_strand == 1) { # On the positive strand.
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1; $seq_region_start = $seq_region_start - $dest_slice_start + 1;
} else { $seq_region_end = $seq_region_end - $dest_slice_start + 1;
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1; # Handle circular chromosomes.
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1; if ( $dest_slice->is_circular() ) {
$seq_region_strand *= -1; if ( $seq_region_start > $seq_region_end ) {
} # Looking at a feature overlapping the chromsome origin.
}
if ( $seq_region_end > $dest_slice_start ) {
#throw away features off the end of the requested slice # Looking at the region in the beginning of the
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length || # chromosome.
( $dest_slice_sr_id != $seq_region_id )) { $seq_region_start -= $dest_slice->seq_region_length();
next FEATURE; }
if ( $seq_region_end < 0 ) {
$seq_region_end += $dest_slice->seq_region_length();
}
} elsif ( $dest_slice_start > $dest_slice_end
&& $seq_region_end < 0 )
{
# Looking at the region overlapping the chromosome
# origin and a feature which is at the beginning of the
# chromosome.
$seq_region_start += $dest_slice->seq_region_length();
$seq_region_end += $dest_slice->seq_region_length();
}
}
} else {
# On the negative strand.
# Handle circular chromosomes.
if ( $dest_slice->is_circular() ) {
if ( $seq_region_start > $seq_region_end ) {
if ( $dest_slice_start > $dest_slice_end ) {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end =
$dest_slice_end +
$dest_slice->seq_region_length -
$tmp_seq_region_start + 1;
} else {
if ( $seq_region_end > $dest_slice_start ) {
# Looking at the region in the beginning of the
# chromosome.
$seq_region_start =
$dest_slice_end - $seq_region_end + 1;
$seq_region_end =
$seq_region_end -
$dest_slice->seq_region_length -
$dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start =
$dest_slice_end -
$seq_region_end -
$dest_slice->seq_region_length + 1;
$seq_region_end =
$dest_slice_end - $tmp_seq_region_start + 1;
}
}
} ## end if ( $seq_region_start...)
} else {
# Non-circular chromosome.
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
}
$seq_region_strand = -$seq_region_strand;
} ## end else [ if ( $dest_slice_strand...)]
# Throw away features off the end of the requested slice.
if ( $seq_region_end < 1
|| $seq_region_start > $dest_slice_length
|| ( $dest_slice_sr_id != $seq_region_id ) )
{
next FEATURE;
} }
$slice = $dest_slice; $slice = $dest_slice;
} } ## end if ( defined($dest_slice...))
# Finally, create the new exon. # Finally, create the new exon.
push( push( @exons,
@exons, $self->_create_feature_fast(
$self->_create_feature_fast( 'Bio::EnsEMBL::Exon', {
'Bio::EnsEMBL::Exon', 'start' => $seq_region_start,
{ 'end' => $seq_region_end,
'start' => $seq_region_start, 'strand' => $seq_region_strand,
'end' => $seq_region_end, 'adaptor' => $self,
'strand' => $seq_region_strand, 'slice' => $slice,
'adaptor' => $self, 'dbID' => $exon_id,
'slice' => $slice, 'stable_id' => $stable_id,
'dbID' => $exon_id, 'version' => $version,
'stable_id' => $stable_id, 'created_date' => $created_date || undef,
'version' => $version, 'modified_date' => $modified_date || undef,
'created_date' => $created_date || undef, 'phase' => $phase,
'modified_date' => $modified_date || undef, 'end_phase' => $end_phase,
'phase' => $phase, 'is_current' => $is_current,
'end_phase' => $end_phase, 'is_constitutive' => $is_constitutive } )
'is_current' => $is_current, );
'is_constitutive' => $is_constitutive
} ) ); } ## end while ( $sth->fetch() )
}
return \@exons; return \@exons;
} } ## end sub _objs_from_sth
=head1 DEPRECATED METHODS =head1 DEPRECATED METHODS
......
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