From 4a33ebbe382ce5e02729b2d1a662301836764925 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 13 Nov 2002 12:25:21 +0000
Subject: [PATCH] Updated Slice PODs Updated slice.t test script
---
modules/Bio/EnsEMBL/Slice.pm | 245 +++++++++++++++++++++++++----------
modules/t/slice.t | 157 +++++++++++++++++++---
2 files changed, 318 insertions(+), 84 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 0ea4b779d0..9071f6b170 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -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) = @_;
diff --git a/modules/t/slice.t b/modules/t/slice.t
index a191ac3ac0..90632cd41e 100644
--- a/modules/t/slice.t
+++ b/modules/t/slice.t
@@ -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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