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Commit 275378ff authored by Ian Longden's avatar Ian Longden
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fixes and STDERR prints added

parent 189f9507
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Showing with 229 additions and 174 deletions
modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
View file @ 275378ff
......@@ -67,7 +67,8 @@ use Bio::EnsEMBL::ChainedAssemblyMapper;
use Bio::EnsEMBL::TopLevelAssemblyMapper;
use Bio::EnsEMBL::Utils::Cache; #CPAN LRU cache
use Bio::EnsEMBL::Utils::Exception qw(deprecate throw);
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
#use Bio::EnsEMBL::Utils::Exception qw(deprecate throw);
use Bio::EnsEMBL::Utils::SeqRegionCache;
use integer; #do proper arithmetic bitshifts
......@@ -574,7 +575,7 @@ sub register_component {
# (2) Use locality of reference (if they want something in same general
# region it will already be registered).
$self->register_assembled($asm_mapper,$asm_seq_region,$asm_start,$asm_end);
$self->register_assembled($asm_mapper,$asm_seq_region_id,$asm_start,$asm_end);
}
......
modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
View file @ 275378ff
......@@ -187,7 +187,7 @@ sub fetch_all_by_Slice_constraint {
throw('Could not retrieve normalized Slices. Database contains ' .
'incorrect assembly_exception information.');
}
# Want to get features on the FULL original slice
# as well as any symlinked slices
......@@ -195,6 +195,10 @@ sub fetch_all_by_Slice_constraint {
# same seq_region as original slice
my $sr_id = $slice->get_seq_region_id();
print STDERR "sr_id = $sr_id\n";
foreach my $pro (@proj){
print STDERR "projected slice -> ".$pro->to_Slice->get_seq_region_id()."\n";
}
@proj = grep { $_->to_Slice->get_seq_region_id() != $sr_id } @proj;
......@@ -217,7 +221,8 @@ sub fetch_all_by_Slice_constraint {
foreach my $seg (@proj) {
my $offset = $seg->from_start();
my $seg_slice = $seg->to_Slice();
print STDERR "MORE: ".$seg_slice->name."\n";
print STDERR "constraint :- $constraint\n";
my $features = $self->_slice_fetch($seg_slice, $constraint); ## NO RESULTS
# if this was a symlinked slice offset the feature coordinates as needed
......@@ -225,6 +230,7 @@ sub fetch_all_by_Slice_constraint {
FEATURE:
foreach my $f (@$features) {
print STDERR "FEAT: ".ref($f)."\n";
if($offset != 1) {
$f->{'start'} += $offset-1;
......@@ -234,6 +240,7 @@ sub fetch_all_by_Slice_constraint {
# discard boundary crossing features from symlinked regions
foreach my $bound (@bounds) {
if($f->{'start'} < $bound && $f->{'end'} >= $bound) {
print STDERR "BOUNDRY CROSSED\n";
next FEATURE;
}
}
......@@ -289,6 +296,7 @@ sub _slice_fetch {
my $slice_strand = $slice->strand();
my $slice_cs = $slice->coord_system();
my $slice_seq_region = $slice->seq_region_name();
my $slice_seq_region_id = $slice->get_seq_region_id();
#get the synonym and name of the primary_table
my @tabs = $self->_tables;
......@@ -300,7 +308,7 @@ sub _slice_fetch {
my $asma = $self->db->get_AssemblyMapperAdaptor();
my @features;
#warn "jere are $self, @feat_css\n";
warn "jere are $self, @feat_css\n";
# fetch the features from each coordinate system they are stored in
COORD_SYSTEM: foreach my $feat_cs (@feat_css) {
my $mapper;
......@@ -334,13 +342,16 @@ sub _slice_fetch {
" AND ${tab_syn}.seq_region_start >= $min_start";
}
print STDERR "#constraint $constraint\n";
my $fs = $self->generic_fetch($constraint,undef,$slice);
# features may still have to have coordinates made relative to slice
# start
print STDERR"#number of features is :- ".scalar(@$fs)."\n";
$fs = _remap($fs, $mapper, $slice);
push @features, @$fs;
print STDERR "#number of features is :- ".scalar(@$fs)."\n";
} else {
$mapper = $asma->fetch_by_CoordSystems($slice_cs, $feat_cs);
......@@ -356,7 +367,8 @@ sub _slice_fetch {
next COORD_SYSTEM if(!@coords);
@ids = map {$_->id()} @coords;
@ids = @{$asma->seq_regions_to_ids($feat_cs, \@ids)};
#coords are now id rather than name
# @ids = @{$asma->seq_regions_to_ids($feat_cs, \@ids)};
# When regions are large and only partially spanned by slice
# it is faster to to limit the query with start and end constraints.
......@@ -369,11 +381,14 @@ sub _slice_fetch {
$constraint .= " AND " if($constraint);
$constraint .= "${tab_syn}.seq_region_id IN ($id_str)";
print STDERR ".con: $constraint\n";
my $fs = $self->generic_fetch($constraint, $mapper, $slice);
print STDERR ".number of features is :- ".scalar(@$fs)."\n";
$fs = _remap($fs, $mapper, $slice);
push @features, @$fs;
print STDERR ".number of features is :- ".scalar(@features)."\n";
} else {
# do multiple split queries using start / end constraints
......@@ -396,9 +411,12 @@ sub _slice_fetch {
" AND ${tab_syn}.seq_region_start >= $min_start";
}
print STDERR "~con: $constraint\n";
my $fs = $self->generic_fetch($constraint,$mapper,$slice);
print STDERR "~number of features is :- ".scalar(@$fs)."\n";
$fs = _remap($fs, $mapper, $slice);
print STDERR "~number after _remap features is :- ".scalar(@$fs)."\n";
push @features, @$fs;
}
......@@ -539,6 +557,7 @@ sub _remap {
my ($seq_region, $start, $end, $strand);
my $slice_seq_region_id = $slice->get_seq_region_id();
my $slice_seq_region = $slice->seq_region_name();
foreach my $f (@$features) {
......@@ -548,13 +567,14 @@ sub _remap {
throw("Feature does not have attached slice.\n");
}
my $fseq_region = $fslice->seq_region_name();
my $fseq_region_id = $fslice->get_seq_region_id();
my $fcs = $fslice->coord_system();
if(!$slice_cs->equals($fcs)) {
#slice of feature in different coord system, mapping required
($seq_region, $start, $end, $strand) =
$mapper->fastmap($fseq_region,$f->start(),$f->end(),$f->strand(),$fcs);
$mapper->fastmap($fseq_region_id,$f->start(),$f->end(),$f->strand(),$fcs);
# undefined start means gap
next if(!defined $start);
......
modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
View file @ 275378ff
......@@ -357,6 +357,7 @@ sub _objs_from_sth {
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
......@@ -364,6 +365,7 @@ sub _objs_from_sth {
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id();
}
FEATURE: while($sth->fetch()) {
......@@ -403,7 +405,7 @@ sub _objs_from_sth {
$seq_region_start = $coords[0]->{'start'};
$seq_region_end = $coords[0]->{'end'};
$sr_name = $coords[0]->{'id'};
$seq_region_id = $coords[0]->{'id'};
if($density_type->value_type() eq 'sum') {
#adjust density value so it reflects length of feature actually used
......@@ -412,15 +414,14 @@ sub _objs_from_sth {
}
#get a slice in the coord system we just mapped to
if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||=
$sa->fetch_by_region($cmp_cs_name, $sr_name,undef, undef, undef,
$cmp_cs_vers);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
$sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
$asm_cs_vers);
}
# if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
# } else {
# $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
# $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
# $asm_cs_vers);
# }
}
#
......@@ -441,7 +442,7 @@ sub _objs_from_sth {
#throw away features entirely off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_name ne $sr_name )) {
( $dest_slice_sr_id ne $seq_region_id )) {
next FEATURE;
}
$slice = $dest_slice;
......
modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
View file @ 275378ff
......@@ -261,6 +261,7 @@ sub _objs_from_sth {
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_seq_region_id;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
......@@ -268,6 +269,7 @@ sub _objs_from_sth {
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_seq_region_id = $dest_slice->get_seq_region_id();
}
FEATURE: while($sth->fetch()) {
......@@ -293,22 +295,20 @@ sub _objs_from_sth {
#
if($mapper) {
($sr_name,$seq_region_start,$seq_region_end,$seq_region_strand) =
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($sr_name));
next FEATURE if(!defined($seq_region_id));
#get a slice in the coord system we just mapped to
if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||=
$sa->fetch_by_region($cmp_cs_name, $sr_name,undef, undef, undef,
$cmp_cs_vers);
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
$sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
$asm_cs_vers);
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
}
}
......@@ -330,7 +330,7 @@ sub _objs_from_sth {
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_name ne $sr_name )) {
( $dest_slice_seq_region_id ne $seq_region_id )) {
next FEATURE;
}
}
......
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
View file @ 275378ff
......@@ -180,8 +180,11 @@ sub fetch_all_by_Transcript {
" AND e.exon_id = et.exon_id";
# fetch all of the exons
print STDERR "\n".$slice."\n\t".$slice->name."\n";
print STDERR "$constraint\n";
my $exons = $self->fetch_all_by_Slice_constraint($slice,$constraint);
print STDERR "ther are ".scalar(@$exons)." exons\n";
#un-override the table definition
$self->{'tables'} = undef;
$self->{'final_clause'} = undef;
......@@ -190,6 +193,7 @@ sub fetch_all_by_Transcript {
if($slice->name() ne $tslice->name()) {
my @out;
foreach my $ex (@$exons) {
print STDERR "$ex being transfered\n";
push @out, $ex->transfer($tslice);
}
$exons = \@out;
......@@ -522,6 +526,7 @@ sub _objs_from_sth {
my $dest_slice_length;
my $dest_slice_cs;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
my $asma;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
......@@ -530,6 +535,7 @@ sub _objs_from_sth {
$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_id = $dest_slice->get_seq_region_id();
$asma = $self->db->get_AssemblyMapperAdaptor();
}
......@@ -565,23 +571,22 @@ sub _objs_from_sth {
#
if($dest_mapper) {
($sr_name,$seq_region_start,$seq_region_end,$seq_region_strand) =
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$dest_mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($sr_name));
next FEATURE if(!defined($seq_region_id));
#get a slice in the coord system we just mapped to
if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||=
$sa->fetch_by_region($cmp_cs_name, $sr_name,undef, undef, undef,
$cmp_cs_vers);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
$sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
$asm_cs_vers);
}
# if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
# } else {
# $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
# $sa->fetch_by_seq_region_id($sr_name, undef, undef, undef,
# $asm_cs_vers);
# }
}
#
......@@ -603,7 +608,7 @@ sub _objs_from_sth {
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_name ne $sr_name )) {
( $dest_slice_sr_id != $seq_region_id )) {
next FEATURE;
}
......
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
View file @ 275378ff
......@@ -1185,12 +1185,15 @@ sub _objs_from_sth {
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id();
}
FEATURE: while($sth->fetch()) {
......@@ -1216,23 +1219,22 @@ sub _objs_from_sth {
#
if($mapper) {
($sr_name,$seq_region_start,$seq_region_end,$seq_region_strand) =
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($sr_name));
next FEATURE if(!defined($seq_region_id));
#get a slice in the coord system we just mapped to
if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||=
$sa->fetch_by_region($cmp_cs_name, $sr_name,undef, undef, undef,
$cmp_cs_vers);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
$sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
$asm_cs_vers);
}
# if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
# } else {
# $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
# $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
# $asm_cs_vers);
# }
}
#
......@@ -1255,7 +1257,7 @@ sub _objs_from_sth {
#throw away features off the end of the requested slice or on different seq_region
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_name ne $sr_name )) {
( $dest_slice_sr_id ne $seq_region_id )) {
next FEATURE;
}
......
modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
View file @ 275378ff
......@@ -338,13 +338,14 @@ sub _objs_from_sth {
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id();
}
my $current = -1;
......@@ -414,27 +415,26 @@ sub _objs_from_sth {
#
if ($mapper) {
($sr_name,$seq_region_start,$seq_region_end,$seq_region_strand) =
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
if(!defined($sr_name)) {
if(!defined($seq_region_id)) {
$throw_away = $misc_feature_id;
next FEATURE;
}
#get a slice in the coord system we just mapped to
if ($asm_cs == $sr_cs ||
($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||=
$sa->fetch_by_region($cmp_cs_name, $sr_name,undef, undef, undef,
$cmp_cs_vers);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
$sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
$asm_cs_vers);
}
# if ($asm_cs == $sr_cs ||
# ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
# } else {
# $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
# $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
# $asm_cs_vers);
# }
}
#
......@@ -455,7 +455,7 @@ sub _objs_from_sth {
}
#throw away features off the end of the requested slice
if ($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_name ne $sr_name )) {
( $dest_slice_sr_id ne $seq_region_id )) {
#flag this feature as one to throw away
$throw_away = $misc_feature_id;
next FEATURE;
......
modules/Bio/EnsEMBL/DBSQL/OligoFeatureAdaptor.pm
View file @ 275378ff
......@@ -306,12 +306,14 @@ sub _objs_from_sth {
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
if ($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id();
}
my $last_feature_id = -1;
......@@ -339,20 +341,20 @@ sub _objs_from_sth {
# Remap the feature coordinates to another coord system if a mapper was provided
if ($mapper) {
($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand)
($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand)
= $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs);
# Skip features that map to gaps or coord system boundaries
next FEATURE if !defined $sr_name;
next FEATURE if !defined $seq_region_id;
# Get a slice in the coord system we just mapped to
if ( $asm_cs == $sr_cs || ( $cmp_cs != $sr_cs && $asm_cs->equals($sr_cs) ) ) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"}
||= $sa->fetch_by_region($cmp_cs_name, $sr_name, undef, undef, undef, $cmp_cs_vers);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"}
||= $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef, $asm_cs_vers);
}
# if ( $asm_cs == $sr_cs || ( $cmp_cs != $sr_cs && $asm_cs->equals($sr_cs) ) ) {
$slice = $slice_hash{"ID:".$seq_region_id}
||= $sa->fetch_by_seq_region_id($seq_region_id);
# } else {
# $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"}
# ||= $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef, $asm_cs_vers);
# }
}
# If a destination slice was provided convert the coords
......@@ -372,7 +374,7 @@ sub _objs_from_sth {
# Throw away features off the end of the requested slice
next FEATURE if $seq_region_end < 1 || $seq_region_start > $dest_slice_length
|| ( $dest_slice_sr_name ne $sr_name );
|| ( $dest_slice_sr_id ne $seq_region_id );
$slice = $dest_slice;
}
......
modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
View file @ 275378ff
......@@ -332,6 +332,7 @@ sub _objs_from_sth {
my $dest_slice_cs;
my $asma;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
......@@ -340,6 +341,7 @@ sub _objs_from_sth {
$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_id = $dest_slice->get_seq_region_id();
$asma = $self->db->get_AssemblyMapperAdaptor();
}
......@@ -377,23 +379,22 @@ sub _objs_from_sth {
#
if($dest_mapper) {
($sr_name,$seq_region_start,$seq_region_end,$seq_region_strand) =
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$dest_mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($sr_name));
next FEATURE if(!defined($seq_region_id));
#get a slice in the coord system we just mapped to
if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||=
$sa->fetch_by_region($cmp_cs_name, $sr_name,undef, undef, undef,
$cmp_cs_vers);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
$sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
$asm_cs_vers);
}
# if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
# } else {
# $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
# $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
# $asm_cs_vers);
# }
}
#
......@@ -415,7 +416,7 @@ sub _objs_from_sth {
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_name ne $sr_name )) {
( $dest_slice_sr_id ne $seq_region_id )) {
next FEATURE;
}
......
modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
View file @ 275378ff
......@@ -304,12 +304,14 @@ sub _objs_from_sth {
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id();
}
FEATURE: while($sth->fetch()) {
......@@ -335,23 +337,22 @@ sub _objs_from_sth {
#
if($mapper) {