From 9126664fe947478e179043431aeb022fc9b148fd Mon Sep 17 00:00:00 2001
From: Daniel Rios <dr2@sanger.ac.uk>
Date: Fri, 28 Apr 2006 09:13:17 +0000
Subject: [PATCH] Modified documentation
---
modules/Bio/EnsEMBL/StrainSlice.pm | 19 +++++++++++++++----
1 file changed, 15 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/StrainSlice.pm b/modules/Bio/EnsEMBL/StrainSlice.pm
index 17b5628d05..22a5e43d54 100644
--- a/modules/Bio/EnsEMBL/StrainSlice.pm
+++ b/modules/Bio/EnsEMBL/StrainSlice.pm
@@ -18,12 +18,24 @@ Bio::EnsEMBL::StrainSlice - SubClass of the Slice. Represents the slice of the g
$slice = $sa->fetch_by_region('chromosome', 'X', 1_000_000, 2_000_000);
- $strainSlice = $slice->get_by_Strain($strain_name);
+ $strainSlice = $slice->get_by_strain($strain_name);
#get the sequence from the Strain Slice
my $seq = $strainSlice->seq();
print $seq;
+ #get differences between this StrainSlice and the reference
+ my $differences = $strainSlice->get_all_differences_Slice();
+ foreach my $difference (@{$differences}){
+ print "Difference in position ", $difference->start,"-",$difference->end," in strain with allele ", $difference->allele_string,"\n";
+ }
+ #compare a strain against another strain
+ my $strainSlice_2 = $slice->get_by_strain($strain_name_2);
+ my $differences = $strainSlice->get_all_differences_StrainSlice($strainSlice_2);
+ foreach my $difference (@{$differences}){
+ print "Difference in position ", $difference->start,"-",$difference->end," in strain with allele ", $difference->allele_string,"\n";
+ }
+
@@ -53,7 +65,6 @@ use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
-use Data::Dumper;
@ISA = qw(Bio::EnsEMBL::Slice);
@@ -188,7 +199,7 @@ sub seq {
Args : nonre
Example : my $differences = $strainSlice->get_all_differences_Slice()
Description : Gets all differences between the StrainSlice object and the Slice is defined
- ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
+ ReturnType : listref of Bio::EnsEMBL::Variation::AlleleFeature
Exceptions : none
Caller : general
@@ -205,7 +216,7 @@ sub get_all_differences_Slice{
Arg[1] : Bio::EnsEMBL::StrainSlice $ss
Example : my $differences = $strainSlice->get_all_differences_StrainSlice($ss)
Description : Gets differences between 2 StrainSlice objects
- ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
+ ReturnType : listref of Bio::EnsEMBL::Variation::AlleleFeature
Exceptions : thrown on bad argument
Caller : general
--
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