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Commit 4a33ebbe authored by Graham McVicker's avatar Graham McVicker
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Updated Slice PODs 

Updated slice.t test script
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modules/Bio/EnsEMBL/Slice.pm
+ 176
− 69
View file @ 4a33ebbe
......@@ -353,9 +353,10 @@ sub subseq {
Arg [1] : (optional) string $logic_name
The name of the analysis used to generate the prediction
transcripts obtained.
Example : @transcripts = $slice->get_all_PredictionTranscripts();
Example : @transcripts = @{$slice->get_all_PredictionTranscripts};
Description: Retrieves the list of prediction transcripts which overlap
this slice.
this slice with logic_name $logic_name. If logic_name is
not defined then all prediction transcripts are retrieved.
Returntype : listref of Bio::EnsEMBL::PredictionTranscript
Exceptions : none
Caller : none
......@@ -379,11 +380,15 @@ sub get_all_PredictionTranscripts {
to obtain.
Arg [2] : (optional) float $score
The mimimum score of the features to retrieve
Example : @dna_align_feats = $slice->get_all_DnaAlignFeatures()
Description: Retrieves the DnaDnaAlignFeatures which overlap this slice
Example : @dna_dna_align_feats = @{$slice->get_all_DnaAlignFeatures};
Description: Retrieves the DnaDnaAlignFeatures which overlap this slice with
logic name $logic_name and with score above $score. If
$logic_name is not defined features of all logic names are
retrieved. If $score is not defined features of all scores are
retrieved.
Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeatures
Exceptions : none
Caller :general
Caller : general
=cut
......@@ -404,9 +409,13 @@ sub get_all_DnaAlignFeatures {
to obtain.
Arg [2] : (optional) float $score
The mimimum score of the features to retrieve
Example : @pep_align_feats = $slice->get_all_ProteinAlignFeatures()
Description: Retrieves the PepDnaAlignFeatures which overlap this slice.
Returntype : listref of Bio::EnsEMBL::PepDnaAlignFeatures
Example : @dna_pep_align_feats = @{$slice->get_all_ProteinAlignFeatures};
Description: Retrieves the DnaPepAlignFeatures which overlap this slice with
logic name $logic_name and with score above $score. If
$logic_name is not defined features of all logic names are
retrieved. If $score is not defined features of all scores are
retrieved.
Returntype : listref of Bio::EnsEMBL::DnaPepAlignFeatures
Exceptions : none
Caller : general
......@@ -428,11 +437,14 @@ sub get_all_ProteinAlignFeatures {
the name of the analysis performed on the features to retrieve
Arg [2] : (optional) float $score
the lower bound of the score of the features to be retrieved
Example : @feats = $slice->get_all_SimilarityFeatures()
Example : @feats = @{$slice->get_all_SimilarityFeatures};
Description: Retrieves all dna_align_features and protein_align_features
with analysis named $logic_name and with score above $score.
It is probably faster to use get_all_ProteinAlignFeatures or
get_all_DnaAlignFeatures if a sepcific feature type is desired.
If $logic_name is not defined features of all logic names are
retrieved. If $score is not defined features of all scores are
retrieved.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
Exceptions : none
Caller : general
......@@ -451,6 +463,7 @@ sub get_all_SimilarityFeatures {
}
=head2 get_all_SimpleFeatures
Arg [1] : (optional) string $logic_name
......@@ -458,9 +471,13 @@ sub get_all_SimilarityFeatures {
to obtain.
Arg [2] : (optional) float $score
The mimimum score of the features to retrieve
Example : @simple_feats = $slice->get_all_SimpleFeatures()
Description: Retrieves the SimpleFeatures which overlap this slice.
Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeature
Example : @simple_feats = @{$slice->get_all_SimpleFeatures};
Description: Retrieves the SimpleFeatures which overlap this slice with
logic name $logic_name and with score above $score. If
$logic_name is not defined features of all logic names are
retrieved. If $score is not defined features of all scores are
retrieved.
Returntype : listref of Bio::EnsEMBL::SimpleFeatures
Exceptions : none
Caller : general
......@@ -481,8 +498,11 @@ sub get_all_SimpleFeatures {
Arg [1] : (optional) string $logic_name
The name of the analysis performed on the repeat features
to obtain.
Example : @repeat_feats = $slice->get_all_RepeatFeatures()
Description: Retrieves the RepeatFeatures which overlap this slice.
Example : @repeat_feats = @{$slice->get_all_RepeatFeatures}
Description: Retrieves the RepeatFeatures which overlap with
logic name $logic_name and with score above $score. If
$logic_name is not defined features of all logic names are
retrieved.
Returntype : listref of Bio::EnsEMBL::RepeatFeatures
Exceptions : none
Caller : general
......@@ -497,13 +517,18 @@ sub get_all_RepeatFeatures {
return $rpfa->fetch_all_by_Slice($self, $logic_name);
}
=head2 get_all_SNPs
Args : none
Function : returns all SNPs on this slice
Function : returns all SNPs on this slice. This function will only work
correctly if the SNP database or the lite database has been
attached to the core database. This can been done through
a call to DBAdaptor::add_db_adaptor.
Returntype: listref of Bio::EnsEMBL::External::Variation
Exceptions: none
Caller : GlyphSet_feature inherited objects
Caller : contigview, snpview
=cut
......@@ -522,13 +547,17 @@ sub get_all_SNPs {
=head2 get_all_Genes
Title : get_all_Genes
Usage :
Function:
Example :
Returns :
Args :
Arg [1] : (optional) boolean $empty_flag
Example : @genes = $slice->get_all_Genes;
Description: Retrieves all genes that overlap this slice. The empty flag is
used by the web code and is used to retrieve light weight genes
that only have a start, end and strand (only works if lite db
is available). If the lite database has been attached to the
core database this method will use the lite database (and
genes will not be as full featured).
Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : none
Caller : none
=cut
......@@ -544,12 +573,20 @@ sub get_all_Genes{
=head2 get_all_Genes_by_source
Arg [1] :
Example :
Description:
Returntype :
Exceptions :
Caller :
Arg [1] : string $source
Arg [2] : (optional) boolean $empty_flag
Example : @genes = @{$slice->get_all_Genes_by_souce('core')};
Description: Retrieves genes that overlap this slice from database $source.
This is primarily used by web code to retrieve subsets of genes
from the lite database (which contains an sets of genes from
several databases). The empty flag indicates light weight
genes that only have a start, end and strand should be used
(only works if lite db is available). If the lite database has
been attached to the core database this method will use the
lite database (and genes will not be as full featured).
Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : none
Caller : contigview
=cut
......@@ -564,12 +601,20 @@ sub get_all_Genes_by_source{
=head2 get_all_Genes_by_type
Arg [1] :
Example :
Description:
Returntype :
Exceptions :
Caller :
Arg [1] : string $type
Arg [2] : (optional) boolean $empty_flag
Example : @genes = @{$slice->get_all_Genes_by_type('ensembl')};
Description: Retrieves genes that overlap this slice of type $type.
This is primarily used by the genebuilding code when several
types of genes are used.
The empty flag indicates light weight genes that only have a
start, end and strand should be used (only works if lite db is
available). If the lite database has
been attached to the core database this method will use the
lite database (and genes will not be as full featured).
Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : none
Caller : genebuilder
=cut
......@@ -583,14 +628,17 @@ sub get_all_Genes_by_type{
=head2 chr_name
Title : chr_name
Usage : $obj->chr_name($newval)
Function:
Example :
Returns : value of chr_name
Args : newvalue (optional)
Arg [1] : (optional) string $value
Example : $chr_name = $slice->chr_name;
Description: Getter/Setter for the name of the chromosome that this slice
is on. This is generally set by the SliceAdaptor and should
probably not be set outside of that context.
Returntype : string
Exceptions : none
Caller : SliceAdaptor
=cut
......@@ -603,15 +651,19 @@ sub chr_name{
}
=head2 chr_start
Title : chr_start
Usage : $obj->chr_start($newval)
Function:
Example :
Returns : value of chr_start
Args : newvalue (optional)
=head2 chr_start
Arg [1] : int $value
Example : $chr_start = $slice->chr_start;
Description: Getter/Setter for the start base of this slice on the
chromosome. This is generally set by the SliceAdaptor and
probably shouldnt be set outside of that context.
chr_start is always less than or equal to chr_end
Returntype : int
Exceptions : none
Caller : SliceAdaptor, general
=cut
......@@ -627,12 +679,15 @@ sub chr_start{
=head2 chr_end
Title : chr_end
Usage : $obj->chr_end($newval)
Function:
Example :
Returns : value of chr_end
Args : newvalue (optional)
Arg [1] : int $value
Example : $chr_end = $slice->chr_end;
Description: Getter/Setter for the end base of this slice on the
chromosome. This is generally set by the SliceAdaptor and
probably shouldnt be set outside of that context.
chr_end is always greater than or equal to chr_start
Returntype : int
Exceptions : none
Caller : SliceAdaptor, general
=cut
......@@ -648,12 +703,14 @@ sub chr_end{
=head2 strand
Title : strand
Usage : $obj->strand($newval)
Function:
Example :
Returns : value of strand
Args : newvalue (optional)
Arg [1] : int $value
Example : $strand = $slice->strand;
Description: Getter/Setter for the strand of the chromosome this slice is on.
This should not be set manually. A much better way to obtain
a slice on the opposite strand is to call the invert method.
Returntype : int (either 1 or -1)
Exceptions : none
Caller : invert, SliceAdaptor, general
=cut
......@@ -671,13 +728,14 @@ sub strand{
=head2 assembly_type
Title : assembly_type
Usage : $obj->assembly_type($newval)
Function:
Example :
Returns : value of assembly_type
Args : newvalue (optional)
Arg [1] : string $value
Example : $assembly_mapper_adaptor->fetch_by_type($slice->assembly_type);
Description: Gets/Sets the assembly type that this slice is constructed
from. This is generally set by the slice adaptor and probably
shouldnt be set outside of this context.
Returntype : string
Exceptions : none
Caller : general
=cut
......@@ -691,6 +749,18 @@ sub assembly_type{
}
=head2 get_all_KaryotypeBands
Arg [1] : none
Example : @kary_bands = @{$slice->get_all_KaryotypeBands};
Description: Retrieves the karyotype bands which this slice overlaps.
Returntype : listref oif Bio::EnsEMBL::KaryotypeBands
Exceptions : none
Caller : general, contigview
=cut
sub get_all_KaryotypeBands {
my ($self) = @_;
......@@ -699,16 +769,28 @@ sub get_all_KaryotypeBands {
}
=head2 get_Chromosome
Arg [1] : none
Example : $chromosome = $slice->get_Chromosome;
Description: Retrieves the chromosome object which this slice is on
Returntype : Bio::EnsEMBL::Chromosome
Exceptions : none
Caller : general
=cut
sub get_Chromosome {
my $self = shift @_;
my $ca = $self->adaptor->db->get_ChromosomeAdaptor();
# this slice will contain N's at the beginning if the chr_start in the table is > 1
return $ca->fetch_by_chr_name($self->chr_name());
}
=head2 get_repeatmasked_seq
Arg [1] : listref of strings $logic_names (optional)
......@@ -754,6 +836,8 @@ sub get_repeatmasked_seq {
return $masked_seq;
}
=head2 _mask_features
Arg [1] : string $dna_string
......@@ -762,7 +846,7 @@ sub get_repeatmasked_seq {
give the list of coordinates to replace with N or with
lower case
Arg [3] : int $soft_masking_enable (optional)
Example :
Example : none
Description: replaces string positions described in the RepeatFeatures
with Ns (default setting), or with the lower case equivalent
(soft masking)
......@@ -822,6 +906,18 @@ sub _mask_features {
}
=head2 get_all_MapFrags
Arg [1] : string $mapset
Example : none
Description: Retreives all mapfrags of mapset $mapset that overlap this slice
Returntype : listref of Bio::EnsEMBL::MapFrags
Exceptions : none
Caller : general
=cut
sub get_all_MapFrags {
my $self = shift;
my $mapset = shift;
......@@ -1061,6 +1157,17 @@ sub get_all_Haplotypes {
=head2 get_all_DASFeatures
Arg [1] : none
Example : $features = $slice->get_all_DASFeatures;
Description: Retreives a hash reference to the DAS features which overlap
this slice
Returntype : hashref of Bio::SeqFeatures
Exceptions : ?
Caller : webcode
=cut
sub get_all_DASFeatures{
my ($self,@args) = @_;
......
modules/t/slice.t
+ 142
− 15
View file @ 4a33ebbe
......@@ -5,7 +5,7 @@ use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 27;
plan tests => 44;
}
......@@ -21,7 +21,7 @@ ok(1);
my $CHR = '20';
my $START = 31_000_000;
my $START = 30_270_000;
my $END = 31_200_000;
my $STRAND = 1;
my $ASSEMBLY_TYPE = 'NCBI_30';
......@@ -116,32 +116,159 @@ ok($slice->strand == $STRAND);
#
# 23-24 Test Slice::seq
#
my $seq = $slice->seq;
my $invert_seq = $slice->invert->seq;
print STDERR "SEQ=[$seq]\n";
my $seq = uc $slice->seq;
my $invert_seq = uc $slice->invert->seq;
ok(length($seq) == $slice->length); #sequence is correct length
print STDERR "[".length($seq)."] != [".$slice->length."]\n";
$seq = uc reverse $seq; #reverse complement seq
$seq =~ s/ACTG/TGAC/g;
$seq = reverse $seq; #reverse complement seq
$seq =~ tr/ACTG/TGAC/;
ok($seq eq $invert_seq); #revcom same as seq on inverted slice
#
# 25-26 Test Slice::subseq
#
my $SPAN = 10;
my $sub_seq = $slice->subseq(-$SPAN,$SPAN);
my $invert_sub_seq = $slice->invert->subseq($slice->length + $SPAN,
$slice->length - $SPAN);
my $sub_seq = uc $slice->subseq(-$SPAN,$SPAN);
my $invert_sub_seq = uc $slice->invert->subseq( $slice->length - $SPAN + 1,
$slice->length + $SPAN + 1);
ok(length $sub_seq == (2*$SPAN) + 1 );
$seq = uc reverse $seq;
$seq =~ s/ACTG/TGAC/g;
ok($seq eq $invert_seq);
$sub_seq = reverse $sub_seq;
$sub_seq =~ tr/ACTG/TGAC/;
ok($sub_seq eq $invert_sub_seq);
#
# 27 Test Slice::get_all_PredictionTranscripts
#
my $pts = $slice->get_all_PredictionTranscripts;
ok(scalar @$pts);
#
# 28 Test Slice::get_all_DnaAlignFeatures
#
my $count = 0;
my $dafs = $slice->get_all_DnaAlignFeatures;
ok(scalar @$dafs);
$count += scalar @$dafs;
#
# 29 Test Slice::get_all_ProteinAlignFeatures
#
my $pafs = $slice->get_all_ProteinAlignFeatures;
ok(scalar @$pafs);
$count += scalar @$pafs;
#
# 30 Test Slice::get_all_SimilarityFeatures
#
ok($count == scalar @{$slice->get_all_SimilarityFeatures});
#
# 31 Test Slice::get_all_SimpleFeatures
#
ok(scalar @{$slice->get_all_SimpleFeatures});
#
# 32 Test Slice::get_all_RepeatFeatures
#
ok(scalar @{$slice->get_all_RepeatFeatures});
#
# 33 Test Slice::get_all_Genes
#
ok(scalar @{$slice->get_all_Genes});
#
# 34 Test Slice::get_all_Genes_by_type
#
ok(scalar @{$slice->get_all_Genes_by_type('ensembl')});
#
# 35 Test Slice::chr_name
#
my $old_val = $slice->chr_name;
my $new_val = 'Y';
$slice->chr_name($new_val);
ok($slice->chr_name eq $new_val);
$slice->chr_name($old_val);
#
# 36 Test Slice::chr_start
#
$old_val = $slice->chr_start;
$new_val = 123;
$slice->chr_start($new_val);
ok($slice->chr_start == $new_val);
$slice->chr_start($old_val);
#
# 37 Test Slice::chr_end
#
$old_val = $slice->chr_end;
$new_val = 1234567;
$slice->chr_end($new_val);
ok($slice->chr_end == $new_val);
$slice->chr_end($old_val);
#
# 38 Test Slice::strand
#
$old_val = $slice->strand;
$new_val = $old_val * -1;
$slice->strand($new_val);
ok($slice->strand == $new_val);
$slice->strand($old_val);
#
# 39 Test Slice::assembly_type
#
$old_val = $slice->assembly_type;
$new_val = 'TEST';
$slice->assembly_type($new_val);
ok($slice->assembly_type eq $new_val);
$slice->assembly_type($old_val);
#
# 40 Test Slice::get_all_KaryotypeBands
#
ok(scalar @{$slice->get_all_KaryotypeBands});
#
# 41-42 Test Slice::get_Chromosome
#
my $chromo;
ok($chromo = $slice->get_Chromosome);
ok($chromo->chr_name eq $slice->chr_name);
#
# 43-44 Test Slice::get_RepeatMaskedSeq
#
$seq = $slice->seq;
ok(length($slice->get_repeatmasked_seq->seq) == length($seq));
my $softmasked_seq = $slice->get_repeatmasked_seq(['RepeatMask'], 1)->seq;
ok($softmasked_seq ne $seq);
ok(uc($softmasked_seq) eq $seq);
$softmasked_seq = $seq = undef;
#
# 45 Test Slice::get_all_MapFrags
#
ok(scalar @{$slice->get_all_MapFrags});
#
# 46 Test Slice::get_tiling_path
#
ok(scalar @{$slice->get_tiling_path});
......
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