diff --git a/modules/Bio/EnsEMBL/DB/RawContigI.pm b/modules/Bio/EnsEMBL/DB/RawContigI.pm
index b5862b2b8bb3f614896293fe26b36ae0a0db9613..153d32016babf1c258cdb3e2c228bb30375e2c44 100755
--- a/modules/Bio/EnsEMBL/DB/RawContigI.pm
+++ b/modules/Bio/EnsEMBL/DB/RawContigI.pm
@@ -93,7 +93,7 @@ sub seq_date{
Usage : $overlap_object = $contig->get_left_overlap();
Function: Returns the overlap object of contig to the left.
This could be undef, indicating no overlap
- Returns : A Bio::EnsEMBL::ContigOverlap object
+ Returns : A Bio::EnsEMBL::ContigOverlapHelper object
Args : None
=cut
@@ -111,7 +111,7 @@ sub get_left_overlap{
Usage : $overlap_object = $contig->get_right_overlap();
Function: Returns the overlap object of contig to the left.
This could be undef, indicating no overlap
- Returns : A Bio::EnsEMBL::ContigOverlap object
+ Returns : A Bio::EnsEMBL::ContigOverlapHelper object
Args : None
=cut
diff --git a/modules/Bio/EnsEMBL/DB/VirtualContig.pm b/modules/Bio/EnsEMBL/DB/VirtualContig.pm
index 2a64447d34e010b18190e1fde01b0b3a4dd45aee..c53a42749c6a1f09848357652d35a7e79600996e 100755
--- a/modules/Bio/EnsEMBL/DB/VirtualContig.pm
+++ b/modules/Bio/EnsEMBL/DB/VirtualContig.pm
@@ -30,9 +30,9 @@ Bio::EnsEMBL::DB::VirtualContig - A virtual contig implementation
# usual contig methods applicable:
- @features = $virtualcontig->get_all_SimilarityFeatures();
- @genes = $virtualcontig->get_all_Genes();
- $seq = $virtualcontig->primary_seq();
+ @features = $virtualcontig->get_all_SimilarityFeatures();
+ @genes = $virtualcontig->get_all_Genes();
+ $seq = $virtualcontig->primary_seq();
# extend methods
@@ -108,26 +108,31 @@ sub _initialize {
$self->_unique_number($VC_UNIQUE_NUMBER);
# set up hashes for the map
- $self->{'start'} = {};
+ $self->{'start'} = {};
$self->{'startincontig'} = {};
- $self->{'contigori'} = {};
- $self->{'feature_skip'} = {};
+ $self->{'contigori'} = {};
+ $self->{'feature_skip'} = {};
# this actually stores the contig we are using
- $self->{'contighash'} = {};
+ $self->{'contighash'} = {};
# this is for cache's of sequence features if/when we want them
- $self->{'_sf_cache'} = {};
+ $self->{'_sf_cache'} = {};
if( defined $clone && defined $focuscontig ){
$self->throw("Build a virtual contig either with a clone or a focuscontig, but not with both");
}
-
+
if( defined $clone ) {
$self->_build_clone_map($clone);
} else {
- if( !defined $focuscontig || !defined $focusposition || !defined $ori || !defined $leftsize || !defined $rightsize ) {
- $self->throw("Have to provide all arguments to virtualcontig \n(focuscontig, focusposition, ori, left and right)");
+ if( !defined $focuscontig ||
+ !defined $focusposition ||
+ !defined $ori ||
+ !defined $leftsize ||
+ !defined $rightsize ) {
+ $self->throw("Have to provide all arguments to virtualcontig \n" .
+ "(focuscontig, focusposition, ori, left and right)");
}
# build the map of how contigs go onto the vc coorindates
@@ -205,6 +210,7 @@ sub primary_seq {
my ($self) = @_;
my $seq = $self->_seq_cache();
+
if( defined $seq ) {
return $seq;
}
@@ -213,26 +219,36 @@ sub primary_seq {
# truncating them and then adding them into the final product.
my @contig_id = sort { $self->{'start'}->{$a} <=> $self->{'start'}->{$b} } keys %{$self->{'start'}};
+
my $seq_string;
my $last_point = 1;
+
foreach my $cid ( @contig_id ) {
- my $c = $self->{'contighash'}->{$cid};
+ print(STDERR "\nFinding sequence for $cid\n");
+ my $c = $self->{'contighash'}->{$cid};
my $tseq = $c->primary_seq();
+
+ print(STDERR "Seq length/start is " . $tseq->length . "\t" .$self->{start}{$cid} . "\n");
if( $self->{'start'}->{$cid} != ($last_point+1) ) {
- # Tony: added a throw here - if we get nagative numbers of inserted N's
- #my $no = $self->{'start'}->{$cid} - $last_point -1;
+ # Tony: added a throw here - if we get negative numbers of inserted N's
+ # my $no = $self->{'start'}->{$cid} - $last_point -1;
+
my $no = $self->{'start'}->{$cid} - $last_point;
+
if ($no < 0){
- $self->throw("Error. Trying to insert negative number ($no) of N\'s into contig sequence");
+ $self->throw("Error. Trying to insert negative number ($no) of N\'s into contig sequence");
}
+
print STDERR "Putting in $no x N\n";
+
$seq_string .= 'N' x $no;
$last_point += $no;
}
my $trunc;
my $end;
+
if( $self->_clone_map == 1 ) {
$end = $c->length;
} else {
@@ -248,29 +264,30 @@ sub primary_seq {
}
}
}
-
- #print STDERR "got $cid, from ",$self->{'startincontig'}->{$cid}," to ",$c->golden_end,"\n";
-
+
+ print STDERR "got $cid, from ",$self->{'startincontig'}->{$cid}," to ",$c->golden_end,"\n";
+
if( $self->{'contigori'}->{$cid} == 1 ) {
-
+ print(STDERR "ori " . $self->{'contigori'}->{$cid} . "\t" . $self->{'startincontig'}->{$cid} . "\t" . $end . "\n");
$trunc = $tseq->subseq($self->{'startincontig'}->{$cid},$end);
} else {
+ print(STDERR "ori " . $self->{'contigori'}->{$cid} . "\t" . $self->{'startincontig'}->{$cid} . "\t" . $end . "\n");
$trunc = $tseq->trunc($end,$self->{'startincontig'}->{$cid})->revcom->seq;
}
- # print STDERR "Got $trunc\n";
+# print STDERR "Got $trunc\n";
$seq_string .= $trunc;
$last_point += length($trunc);
}
- $seq = Bio::PrimarySeq->new( -id => "virtual_contig_".$self->_unique_number,
- -seq => $seq_string,
+ $seq = Bio::PrimarySeq->new( -id => "virtual_contig_".$self->_unique_number,
+ -seq => $seq_string,
-moltype => 'dna'
);
-
+
$self->_seq_cache($seq);
-
+
return $seq;
}
@@ -292,18 +309,6 @@ sub id{
return "virtual_contig_".$self->_unique_number;
}
-=head2 get_all_SeqFeatures
-
- Title : get_all_SeqFeatures
- Usage : foreach my $sf ( $contig->get_all_SeqFeatures )
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
=head2 top_SeqFeatures
Title : top_SeqFeatures
@@ -342,12 +347,23 @@ sub top_SeqFeatures{
}
+=head2 get_all_SeqFeatures
+
+ Title : get_all_SeqFeatures
+ Usage : foreach my $sf ( $contig->get_all_SeqFeatures )
+ Function:
+ Example :
+ Returns :
+ Args :
+
+
+=cut
+
sub get_all_SeqFeatures{
my ($self) = @_;
my @out;
push(@out,$self->get_all_SimilarityFeatures());
push(@out,$self->get_all_RepeatFeatures());
- # push(@out,$self->
return @out;
@@ -389,7 +405,6 @@ sub get_all_RepeatFeatures{
return $self->_get_all_SeqFeatures_type('repeat');
-
}
@@ -407,48 +422,48 @@ sub get_all_RepeatFeatures{
=cut
sub get_all_Genes{
- my ($self) = @_;
- my (%gene,%trans,%exon);
-
- foreach my $c ( values %{$self->{'contighash'}} ) {
- foreach my $gene ( $c->get_all_Genes() ) {
- $gene{$gene->id()} = $gene;
- }
- }
-
- # get out unique set of translation objects
- foreach my $gene ( values %gene ) {
- foreach my $transcript ( $gene->each_Transcript ) {
- my $translation = $transcript->translation;
- $trans{"$translation"} = $translation;
-
- }
- }
-
- foreach my $gene ( values %gene ) {
- foreach my $exon ( $gene->all_Exon_objects() ) {
- # hack to get things to behave
- print STDERR "Exon was ",$exon->start,":",$exon->end,":",$exon->strand,"\n";
- $exon->seqname($exon->contig_id);
- $exon{$exon->id} = $exon;
- $self->_convert_seqfeature_to_vc_coords($exon);
- print STDERR "Exon going to ",$exon->start,":",$exon->end,":",$exon->strand," ,",$exon->seqname,"\n";
- }
- }
-
- foreach my $t ( values %trans ) {
- my ($start,$end,$str) = $self->_convert_start_end_strand_vc($exon{$t->start_exon_id}->contig_id,$t->start,$t->start,1);
- $t->start($start);
- ($start,$end,$str) = $self->_convert_start_end_strand_vc($exon{$t->end_exon_id}->contig_id,$t->end,$t->end,1);
- $t->end($start);
- }
+ my ($self) = @_;
+ my (%gene,%trans,%exon);
- return values %gene;
+ foreach my $c ( values %{$self->{'contighash'}} ) {
+ foreach my $gene ( $c->get_all_Genes() ) {
+ $gene{$gene->id()} = $gene;
+ }
+ }
+
+ # get out unique set of translation objects
+ foreach my $gene ( values %gene ) {
+ foreach my $transcript ( $gene->each_Transcript ) {
+ my $translation = $transcript->translation;
+ $trans{"$translation"} = $translation;
+
+ }
+ }
+
+ foreach my $gene ( values %gene ) {
+ foreach my $exon ( $gene->all_Exon_objects() ) {
+ # hack to get things to behave
+ print STDERR "Exon was ",$exon->start,":",$exon->end,":",$exon->strand,"\n";
+ $exon->seqname($exon->contig_id);
+ $exon{$exon->id} = $exon;
+ $self->_convert_seqfeature_to_vc_coords($exon);
+ print STDERR "Exon going to ",$exon->start,":",$exon->end,":",$exon->strand," ,",$exon->seqname,"\n";
+ }
+ }
+
+ foreach my $t ( values %trans ) {
+ my ($start,$end,$str) = $self->_convert_start_end_strand_vc($exon{$t->start_exon_id}->contig_id,$t->start,$t->start,1);
+ $t->start($start);
+ ($start,$end,$str) = $self->_convert_start_end_strand_vc($exon{$t->end_exon_id}->contig_id,$t->end,$t->end,1);
+ $t->end($start);
+ }
+
+ return values %gene;
}
=head2 length
-
+
Title : length
Usage :
Function: Provides the length of the contig
@@ -547,19 +562,25 @@ sub skip_SeqFeature{
sub _build_clone_map{
my ($self,$clone) = @_;
- my ($tlen,$length);
- $tlen = $length = 0;
- my $seen = 0;
+
+ my $tlen = 0;
+ my $length = 0;
+ my $seen = 0;
+
foreach my $contig ( $clone->get_all_Contigs ) {
- $self->{'start'}->{$contig->id} = $contig->embl_offset;
+ $self->{'start'} ->{$contig->id} = $contig->embl_offset;
$self->{'startincontig'}->{$contig->id} = 1;
- $self->{'contigori'}->{$contig->id} = 1;
- $self->{'contighash'}->{$contig->id} = $contig;
+ $self->{'contigori'} ->{$contig->id} = 1;
+ $self->{'contighash'} ->{$contig->id} = $contig;
+
print STDERR "Got ",$contig->id," [",$contig->embl_offset,"] to [",$contig->length,"]\n";
+
$tlen = $contig->embl_offset+$contig->length;
+
if( $tlen > $length ) {
$length = $tlen;
}
+
if( $seen == 0 ) {
$self->dbobj($contig->dbobj);
$seen = 1;
@@ -590,192 +611,216 @@ sub _build_clone_map{
=cut
sub _build_contig_map{
- my ($self,$focuscontig,$focusposition,$ori,$left,$right) = @_;
+ my ($self,$focuscontig,$focusposition,$ori,$left,$right) = @_;
# we first need to walk down contigs going left
# so we can figure out the start position (contig-wise)
# initialisation - find the correct end of the focus contig
- my ($current_left_size,$current_orientation,$current_contig,$overlap);
-
- if( $ori == 1 ) {
- $current_left_size = $focusposition;
- $current_orientation = 1;
- } else {
- $current_left_size = $focuscontig->length - $focusposition;
- $current_orientation = -1;
- }
- $current_contig = $focuscontig;
-
- while( $current_left_size < $left ) {
- print STDERR "Looking at ",$current_contig->id," with $current_left_size\n";
-
- if( $current_orientation == 1 ) {
-
- # go left wrt to the contig.
- $overlap = $current_contig->get_left_overlap();
- # if there is no left overlap, trim left to this size
- # as this means we have run out of contigs
-
- print STDERR "Gone left\n";
-
- if( !defined $overlap ) {
- $left = $current_left_size;
- print STDERR "getting out - no overlap\n";
- last;
- }
-
-
- if( $overlap->distance == 0 ) {
- # The mystic -1 here is because otherwise we double count the
- # switch point base
- $current_left_size += $overlap->sister->golden_length -1;
- } else {
- $current_left_size += $overlap->distance;
- $current_left_size += $overlap->sister->golden_length;
- }
-
- $current_contig = $overlap->sister();
-
- if( $overlap->sister_polarity == 1) {
- $current_orientation = 1;
- } else {
- $current_orientation = -1;
- }
- } else {
- # go right wrt to the contig.
- $overlap = $current_contig->get_right_overlap();
- # if there is no left overlap, trim left to this size
- # as this means we have run out of contigs
- if( !defined $overlap ) {
- $left = $current_left_size;
- last;
- }
-
- if( $overlap->distance == 0 ) {
- # The mystic -1 here is because otherwise we double count the
- # switch point base
- $current_left_size += $overlap->sister->golden_length-1;
- } else {
- $current_left_size += $overlap->distance;
- $current_left_size += $overlap->sister->golden_length;
- }
-
- $current_contig = $overlap->sister();
-
- if( $overlap->sister_polarity == 1) {
- $current_orientation = -1;
- } else {
- $current_orientation = 1;
- }
- }
- }
-
-
+ my ($current_left_size,$current_orientation,$current_contig,$overlap);
+
+ if( $ori == 1 ) {
+ $current_left_size = $focusposition;
+ $current_orientation = 1;
+ } else {
+ $current_left_size = $focuscontig->length - $focusposition;
+ $current_orientation = -1;
+ }
- # now $current_contig is the left most contig in this set, with
- # its orientation set and ready to rock... ;)
+ $current_contig = $focuscontig;
+
+ print STDERR "Left size is $left\n";
+
+ while( $current_left_size < $left ) {
+ print(STDERR "Current left = $current_left_size\n");
+ print STDERR "Looking at ",$current_contig->id," with $current_left_size\n";
+
+ if( $current_orientation == 1 ) {
+
+ # go left wrt to the contig.
+ $overlap = $current_contig->get_left_overlap();
+
+
+ # if there is no left overlap, trim left to this size
+ # as this means we have run out of contigs
+
+ print STDERR "Gone left\n";
+
+ if( !defined $overlap ) {
+ $left = $current_left_size;
+ print STDERR "getting out - no overlap\n";
+ last;
+ }
+
+
+ if( $overlap->distance == 0 ) {
+ # The mystic -1 here is because otherwise we double count the
+ # switch point base
+ $current_left_size += $overlap->sister->golden_length -1;
+ } else {
+ $current_left_size += $overlap->distance;
+ $current_left_size += $overlap->sister->golden_length;
+ }
+
+ $current_contig = $overlap->sister();
+
+ if( $overlap->sister_polarity == 1) {
+ $current_orientation = 1;
+ } else {
+ $current_orientation = -1;
+ }
+ } else {
+ # go right wrt to the contig.
+ $overlap = $current_contig->get_right_overlap();
+
+ # if there is no left overlap, trim left to this size
+ # as this means we have run out of contigs
+ if( !defined $overlap ) {
+ $left = $current_left_size;
+ last;
+ }
+
+ if( $overlap->distance == 0 ) {
+ # The mystic -1 here is because otherwise we double count the
+ # switch point base
+ $current_left_size += $overlap->sister->golden_length-1;
+ } else {
+ $current_left_size += $overlap->distance;
+ $current_left_size += $overlap->sister->golden_length;
+ }
+
+ $current_contig = $overlap->sister();
+
+ if( $overlap->sister_polarity == 1) {
+ $current_orientation = -1;
+ } else {
+ $current_orientation = 1;
+ }
+ }
+ }
+
+
+ # now $current_contig is the left most contig in this set, with
+ # its orientation set and ready to rock... ;)
+
my $total = $left + $right;
-
- print STDERR "leftmost contig is ",$current_contig->id," with $total to account for, gone $current_left_size of $left\n";
+
+ print STDERR "leftmost contig is ",$current_contig->id," with $total to account for, gone $current_left_size of $left\n";
$self->{'leftmostcontig_id'} = $current_contig->id;
# the first contig will need to be trimmed at a certain point
- my $startpos;
- if( $current_orientation == 1 ) {
- $startpos = $current_contig->golden_start + ($current_left_size - $left);
- } else {
- $startpos = $current_contig->golden_end - ($current_left_size - $left);
- }
+
+
+ my $startpos;
print STDERR "Leftmost contig starts at: $startpos orientation: $current_orientation\n";
print STDERR "Current left = $left vs global left= $current_left_size\n";
- $self->{'start'}->{$current_contig->id} = 1;
- $self->{'startincontig'}->{$current_contig->id} = $startpos;
- $self->{'contigori'}->{$current_contig->id} = $current_orientation;
- $self->{'contighash'}->{$current_contig->id} = $current_contig;
+ if( $current_orientation == 1 ) {
+ print(STDERR "Current orientation $current_orientation\n");
+ print(STDERR "golden start " . $current_contig->golden_start . "\n");
+ $startpos = $current_contig->golden_start + ($current_left_size - $left);
+ } else {
+ print(STDERR "Current orientation $current_orientation\n");
+ print(STDERR "golden end " . $current_contig->golden_end . "\n");
+ $startpos = $current_contig->golden_end - ($current_left_size - $left);
+ }
+
+ print STDERR "Leftmost contig has $startpos and $current_orientation $left vs $current_left_size\n";
+
+ $self->{'start'} ->{$current_contig->id} = 1;
+ $self->{'startincontig'}->{$current_contig->id} = $startpos;
+ $self->{'contigori'} ->{$current_contig->id} = $current_orientation;
+ $self->{'contighash'} ->{$current_contig->id} = $current_contig;
+
my $current_length;
- if( $current_orientation == 1 ) {
- # mystic +1 due to biological counting scheme
- $current_length = $current_contig->golden_end - $startpos +1;
- } else {
- # mystic +1 due to biological counting scheme
- $current_length = $startpos - $current_contig->golden_start+1;
- }
- print STDERR "current length before we get into this is $current_length\n";
-
-
- while( $current_length < $total ) {
- print STDERR "In building actually got $current_length towards $total\n";
-
- # move onto the next contig.
-
- if( $current_orientation == 1 ) {
- # go right wrt to the contig.
- print STDERR "Going right\n";
-
- $overlap = $current_contig->get_right_overlap();
-
- # if there is no right overlap, trim right to this size
- # as this means we have run out of contigs
- if( !defined $overlap ) {
- print STDERR "Out of contigs!\n";
-
- $right = $current_length - $left;
- last;
- }
-
- # add to total, move on the contigs
-
- $current_contig = $overlap->sister();
- $self->{'contighash'}->{$current_contig->id} = $current_contig;
-
- if( $overlap->sister_polarity == 1) {
- $current_orientation = 1;
- } else {
- $current_orientation = -1;
- }
-
- # The +1's here are to handle the fact we want to produce abutting
- # coordinate systems from overlapping switch points.
- if( $overlap->distance == 0 ) {
- $self->{'start'}->{$current_contig->id} = $current_length +1;
- } else {
- $self->{'start'}->{$current_contig->id} = $current_length + $overlap->distance;
- $current_length += $overlap->distance;
- }
-
- if( $current_orientation == 1 ) {
- $self->{'startincontig'}->{$current_contig->id} = $current_contig->golden_start+1;
- } else {
- $self->{'startincontig'}->{$current_contig->id} = $current_contig->golden_end-1;
+ if( $current_orientation == 1 ) {
+ # mystic +1 due to biological counting scheme
+ $current_length = $current_contig->golden_end - $startpos +1;
+ } else {
+ # mystic +1 due to biological counting scheme
+ $current_length = $startpos - $current_contig->golden_start+1;
+ }
+ print STDERR "current length before we get into this is $current_length\n";
+
+ while( $current_length < $total ) {
+ print STDERR "In building actually got $current_length towards $total\n";
+
+ # move onto the next contig.
+
+ if( $current_orientation == 1 ) {
+ # go right wrt to the contig.
+ print STDERR "Going right\n";
+
+ $overlap = $current_contig->get_right_overlap();
+
+ # if there is no right overlap, trim right to this size
+ # as this means we have run out of contigs
+ if( !defined $overlap ) {
+ print STDERR "Out of contigs!\n";
+
+ $right = $current_length - $left;
+ last;
}
-
- $self->{'contigori'}->{$current_contig->id} = $current_orientation;
-
- # up the length
- $current_length += $overlap->sister->golden_length -1;
- } else {
- # go left wrt to the contig
- print STDERR "Going left\n";
-
- $overlap = $current_contig->get_left_overlap();
+
+ # add to total, move on the contigs
+
+ $current_contig = $overlap->sister();
+ print(STDERR "New sister " . $current_contig->id . "\n");
+ $self->{'contighash'}->{$current_contig->id} = $current_contig;
+
+ if( $overlap->sister_polarity == 1) {
+ $current_orientation = 1;
+ } else {
+ $current_orientation = -1;
+ }
+
+ # The +1's here are to handle the fact we want to produce abutting
+ # coordinate systems from overlapping switch points.
+ if( $overlap->distance == 0 ) {
+ $self->{'start'}->{$current_contig->id} = $current_length +1;
+ } else {
+ $self->{'start'}->{$current_contig->id} = $current_length + $overlap->distance;
+ $current_length += $overlap->distance;
+ }
+
+ if( $current_orientation == 1 ) {
+ print(STDERR "Current orientation $current_orientation\n");
+ print(STDERR "golden start " . $current_contig->golden_start . "\n");
+
+ $self->{'startincontig'}->{$current_contig->id} = $current_contig->golden_start+1;
+ } else {
+ print(STDERR "Current orientation $current_orientation\n");
+ print(STDERR "golden end " . $current_contig->golden_end . "\n");
+
+ $self->{'startincontig'}->{$current_contig->id} = $current_contig->golden_end-1;
+ }
+
+ $self->{'contigori'}->{$current_contig->id} = $current_orientation;
+
+ # up the length
+ $current_length += $overlap->sister->golden_length -1;
+ } else {
+ # go left wrt to the contig
+ print STDERR "Going left with " . $current_contig->id . "\n";
+
+ $overlap = $current_contig->get_left_overlap();
- # if there is no left overlap, trim right to this size
- # as this means we have run out of contigs
- if( !defined $overlap ) {
- $right = $current_length - $left;
- last;
- }
+ # if there is no left overlap, trim right to this size
+ # as this means we have run out of contigs
+ if( !defined $overlap ) {
+ $right = $current_length - $left;
+ last;
+ }
# add to total, move on the contigs
$current_contig = $overlap->sister();
+ print(STDERR "New sister " . $current_contig->id . "\n");
$self->{'contighash'}->{$current_contig->id} = $current_contig;
if( $overlap->sister_polarity == 1) {
@@ -840,7 +885,7 @@ sub _build_contig_map{
Title : _get_all_SeqFeatures_type
Usage : Internal function which encapsulates getting
features of a particular type and returning
- them in the VC coordinates, optionally cache'ing
+ them in the VC coordinates, optionally cacheing
them.
Function:
Example :