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Commit 044be9f6 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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_objs_from_sth(): Readability.

parent 79f94a99
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Showing with 107 additions and 88 deletions
modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
View file @ 044be9f6
......@@ -366,7 +366,7 @@ sub save {
=cut
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
......@@ -374,9 +374,11 @@ sub _objs_from_sth {
# a fair bit of gymnastics is used.
#
# in case of userdata we need the features on the dest_slice
# in case of get_all_supporting_features dest_slice is not provided ..
my $sa = $dest_slice ? $dest_slice->adaptor() : $self->db()->get_SliceAdaptor();
# In case of userdata we need the features on the dest_slice. In case
# of get_all_supporting_features dest_slice is not provided.
my $sa = ( $dest_slice
? $dest_slice->adaptor()
: $self->db()->get_SliceAdaptor() );
my $aa = $self->db->get_AnalysisAdaptor();
my @features;
......@@ -385,18 +387,28 @@ sub _objs_from_sth {
my %sr_name_hash;
my %sr_cs_hash;
my($dna_align_feature_id, $seq_region_id, $analysis_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $hit_start, $hit_end, $hit_name,
$hit_strand, $cigar_line, $evalue, $perc_ident, $score,
$external_db_id, $hcoverage, $extra_data, $pair_dna_align_feature_id,
$external_db_name, $external_display_db_name);
$sth->bind_columns(
\$dna_align_feature_id, \$seq_region_id, \$analysis_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$hit_start, \$hit_end, \$hit_name,
\$hit_strand, \$cigar_line, \$evalue, \$perc_ident, \$score,
\$external_db_id, \$hcoverage, \$extra_data, \$pair_dna_align_feature_id,
\$external_db_name, \$external_display_db_name);
my ( $dna_align_feature_id, $seq_region_id,
$analysis_id, $seq_region_start,
$seq_region_end, $seq_region_strand,
$hit_start, $hit_end,
$hit_name, $hit_strand,
$cigar_line, $evalue,
$perc_ident, $score,
$external_db_id, $hcoverage,
$extra_data, $pair_dna_align_feature_id,
$external_db_name, $external_display_db_name );
$sth->bind_columns( \( $dna_align_feature_id, $seq_region_id,
$analysis_id, $seq_region_start,
$seq_region_end, $seq_region_strand,
$hit_start, $hit_end,
$hit_name, $hit_strand,
$cigar_line, $evalue,
$perc_ident, $score,
$external_db_id, $hcoverage,
$extra_data, $pair_dna_align_feature_id,
$external_db_name, $external_display_db_name )
);
my $asm_cs;
my $cmp_cs;
......@@ -404,9 +416,10 @@ sub _objs_from_sth {
my $asm_cs_name;
my $cmp_cs_vers;
my $cmp_cs_name;
if($mapper) {
$asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
if ( defined($mapper) ) {
$asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
......@@ -420,76 +433,79 @@ sub _objs_from_sth {
my $dest_slice_sr_name;
my $dest_slice_seq_region_id;
if($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 = $dest_slice->seq_region_name();
if ( defined($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_seq_region_id = $dest_slice->get_seq_region_id();
}
FEATURE: while($sth->fetch()) {
#get the analysis object
FEATURE:
while ( $sth->fetch() ) {
# Get the analysis object.
my $analysis = $analysis_hash{$analysis_id} ||=
$aa->fetch_by_dbID($analysis_id);
#get the slice object
my $slice = $slice_hash{"ID:".$seq_region_id};
# Get the slice object.
my $slice = $slice_hash{ "ID:" . $seq_region_id };
if(!$slice) {
if ( !defined($slice) ) {
$slice = $sa->fetch_by_seq_region_id($seq_region_id);
if ($slice) {
$slice_hash{"ID:".$seq_region_id} = $slice;
if ( defined($slice) ) {
$slice_hash{ "ID:" . $seq_region_id } = $slice;
$sr_name_hash{$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();
}
}
my $sr_name = $sr_name_hash{$seq_region_id};
my $sr_cs = $sr_cs_hash{$seq_region_id};
#
# remap the feature coordinates to another coord system
# if a mapper was provided
#
if($mapper) {
($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, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($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 = $slice_hash{"ID:".$seq_region_id} ||=
# Remap the feature coordinates to another coord system
# if a mapper was provided.
if ( defined($mapper) ) {
( $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, $sr_cs );
# Skip features that map to gaps or coord system boundaries.
if ( !defined($seq_region_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{ "ID:" . $seq_region_id } ||=
$sa->fetch_by_seq_region_id($seq_region_id);
} else {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$slice = $slice_hash{ "ID:" . $seq_region_id } ||=
$sa->fetch_by_seq_region_id($seq_region_id);
}
}
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) {
if($dest_slice_strand == 1) {
# If a destination slice was provided, convert the coords. If the
# dest_slice starts at 1 and is foward strand, nothing needs doing.
if ( defined($dest_slice) ) {
if ( $dest_slice_start != 1 || $dest_slice_strand != 1 ) {
if ( $dest_slice_strand == 1 ) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
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_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
}
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_seq_region_id ne $seq_region_id )) {
# Throw away features off the end of the requested slice.
if ( $seq_region_end < 1
|| $seq_region_start > $dest_slice_length
|| ( $dest_slice_seq_region_id ne $seq_region_id ) )
{
next FEATURE;
}
}
......@@ -499,34 +515,37 @@ sub _objs_from_sth {
# Finally, create the new DnaAlignFeature.
push( @features,
$self->_create_feature_fast(
'Bio::EnsEMBL::DnaDnaAlignFeature', {
'slice' => $slice,
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'hseqname' => $hit_name,
'hstart' => $hit_start,
'hend' => $hit_end,
'hstrand' => $hit_strand,
'score' => $score,
'p_value' => $evalue,
'percent_id' => $perc_ident,
'cigar_string' => $cigar_line,
'analysis' => $analysis,
'adaptor' => $self,
'dbID' => $dna_align_feature_id,
'external_db_id' => $external_db_id,
'hcoverage' => $hcoverage,
'extra_data' => $extra_data ? $self->get_dumped_data($extra_data) : '',
'dbname' => $external_db_name,
'db_display_name' => $external_display_db_name,
'pair_dna_align_feature_id' => $pair_dna_align_feature_id
} ) );
}
'Bio::EnsEMBL::DnaDnaAlignFeature', {
'slice' => $slice,
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'hseqname' => $hit_name,
'hstart' => $hit_start,
'hend' => $hit_end,
'hstrand' => $hit_strand,
'score' => $score,
'p_value' => $evalue,
'percent_id' => $perc_ident,
'cigar_string' => $cigar_line,
'analysis' => $analysis,
'adaptor' => $self,
'dbID' => $dna_align_feature_id,
'external_db_id' => $external_db_id,
'hcoverage' => $hcoverage,
'extra_data' => (
$extra_data
? $self->get_dumped_data($extra_data)
: '' ),
'dbname' => $external_db_name,
'db_display_name' => $external_display_db_name,
'pair_dna_align_feature_id' => $pair_dna_align_feature_id
} ) );
} ## end while ( $sth->fetch() )
return \@features;
}
} ## end sub _objs_from_sth
=head2 list_dbIDs
......
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