From a959ef85e0ffdfbb046d323580c8b783e7b6ae2a Mon Sep 17 00:00:00 2001
From: Daniel Rios <dr2@sanger.ac.uk>
Date: Thu, 28 Jun 2007 07:42:49 +0000
Subject: [PATCH] added argument in seq method to return sequence with coverage
information if set to 1
---
modules/Bio/EnsEMBL/StrainSlice.pm | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/StrainSlice.pm b/modules/Bio/EnsEMBL/StrainSlice.pm
index 3145fa3181..b7115821f6 100644
--- a/modules/Bio/EnsEMBL/StrainSlice.pm
+++ b/modules/Bio/EnsEMBL/StrainSlice.pm
@@ -217,10 +217,11 @@ sub display_Slice_name{
=head2 seq
- Arg [1] : none
+ Arg [1] : int $with_coverage (optional)
Example : print "SEQUENCE = ", $strainSlice->seq();
Description: Returns the sequence of the region represented by this
- slice formatted as a string in the strain.
+ slice formatted as a string in the strain. If flag with_coverage
+ is set to 1, returns sequence if there is coverage in the region
Returntype : string
Exceptions : none
Caller : general
@@ -229,6 +230,9 @@ sub display_Slice_name{
sub seq {
my $self = shift;
+ my $with_coverage = shift;
+
+ $with_coverage ||= 0;
# special case for in-between (insert) coordinates
return '' if($self->start() == $self->end() + 1);
@@ -250,7 +254,7 @@ sub seq {
#need to find coverage information if different from reference
my $indAdaptor = $self->adaptor->db->get_db_adaptor('variation')->get_IndividualAdaptor;
my $ref_strain = $indAdaptor->get_reference_strain_name;
- $self->_add_coverage_information($reference_sequence) if ($self->strain_name ne $ref_strain);
+ $self->_add_coverage_information($reference_sequence) if ($with_coverage == 1 && $self->strain_name ne $ref_strain);
return substr(${$reference_sequence},0,1) if ($self->length == 1);
return ${$reference_sequence}; #returns the reference sequence, applying the variationFeatures
}
@@ -290,7 +294,7 @@ sub _add_coverage_information{
=head2 get_all_AlleleFeatures_Slice
- Args : nonre
+ Args : none
Example : my $af = $strainSlice->get_all_AlleleFeatures_Slice()
Description : Gets all AlleleFeatures between the StrainSlice object and the Slice is defined
ReturnType : listref of Bio::EnsEMBL::Variation::AlleleFeature
--
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