From 201cea309ba87815e3fd69f8dc3b5c9de9e911b7 Mon Sep 17 00:00:00 2001
From: Felix Kokocinski <fsk@sanger.ac.uk>
Date: Wed, 20 Sep 2006 13:11:33 +0000
Subject: [PATCH] bugtweak
---
modules/Bio/EnsEMBL/Map/DitagFeature.pm | 32 +++++++++++++++----------
1 file changed, 20 insertions(+), 12 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Map/DitagFeature.pm b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
index b0b49e24eb..502a145496 100644
--- a/modules/Bio/EnsEMBL/Map/DitagFeature.pm
+++ b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
@@ -81,7 +81,7 @@ sub new {
my ($caller, @args) = @_;
my ( $dbID, $adaptor, $start, $end, $strand, $slice, $analysis, $hit_start, $hit_end,
$hit_strand, $ditag_id, $ditag_side, $cigar_line, $ditag_pair_id, $tag_count ) = rearrange(
- [ 'dbid', 'adaptor' ,'start', 'end', 'strand', 'slice', 'analysis', 'hit_start',
+ [ 'dbid', 'adaptor' ,'start', 'end', 'strand', 'slice', 'analysis', 'hit_start',
'hit_end', 'hit_strand', 'ditag_id', 'ditag_side', 'cigar_line', 'ditag_pair_id' ,'tag_count'],
@args );
my $class = ref($caller) || $caller;
@@ -97,9 +97,9 @@ sub new {
throw('-STRAND argument must be 1, -1, or 0');
}
}
- if(defined($hit_strand)) {
+ if(defined($hit_strand)) {
if(!($hit_strand == 1) && !($hit_strand == -1) && !($hit_strand == 0)) {
- throw('-HIT_STRAND argument must be 1, -1, or 0');
+ throw('-HIT_STRAND argument must be 1, -1, or 0 not '.$hit_strand);
}
}
if(defined($start) && defined($end)) {
@@ -165,6 +165,7 @@ sub fetch_ditag {
this DitagFeature belongs to.
If it is not a paired ditag, these will be identical
to DitagFeature->start() & DitagFeature->end().
+ Please note that the returned start/end are min/max locations.
Returntype : int (start, end, strand)
Exceptions : throws if the 2 features of a pair are found on different strands
or if the second one cannot be found.
@@ -181,18 +182,25 @@ sub get_ditag_location {
$end = $self->end;
}
else{
- my ($ditag_a, $ditag_b);
+ my ($ditag_a, $ditag_b, $more);
eval{
- ($ditag_a, $ditag_b) = @{$self->adaptor->fetch_all_by_ditagID($self->ditag_id, $self->ditag_pair_id)};
+ ($ditag_a, $ditag_b, $more) = @{$self->adaptor->fetch_all_by_ditagID($self->ditag_id, $self->ditag_pair_id)};
};
- if($@ or !defined($ditag_b)){
- throw("Cannot find 2nd tag of pair (".$self->dbID.", ".$self->ditag_id.", ".$self->ditag_pair_id.")");
+ if($@ or !defined($ditag_a) or !defined($ditag_b)){
+ #warn("Cannot find 2nd tag of pair (".$self->dbID.", ".$self->ditag_id.", ".$self->ditag_pair_id.")");
+ $start = $self->start;
+ $end = $self->end;
}
-
- ($ditag_a->start < $ditag_b->start) ? ($start = $ditag_a->start) : ($start = $ditag_b->start);
- ($ditag_a->end > $ditag_b->end) ? ($end = $ditag_a->end) : ($end = $ditag_b->end);
- if($self->strand != $ditag_b->strand){
- throw('the strand of the two ditagFeatures are different! '.$ditag_a->strand.'/'.$ditag_b->strand);
+ else{
+ if(defined $more){
+ throw("More than two DitagFeatures were returned for ".$self->dbID.", ".$self->ditag_id.", ".$self->ditag_pair_id);
+ }
+
+ ($ditag_a->start < $ditag_b->start) ? ($start = $ditag_a->start) : ($start = $ditag_b->start);
+ ($ditag_a->end > $ditag_b->end) ? ($end = $ditag_a->end) : ($end = $ditag_b->end);
+ if($ditag_a->strand != $ditag_b->strand){
+ throw('the strand of the two ditagFeatures are different! '.$ditag_a->strand.'/'.$ditag_b->strand);
+ }
}
}
--
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