Commit 9126664f authored by Daniel Rios's avatar Daniel Rios
Browse files

Modified documentation

parent e7a99268
......@@ -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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