From 01fd5893b4040fba35605158e75e15faf6cb3680 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Tue, 12 Jul 2011 15:23:54 +0000
Subject: [PATCH] Added a summary_as_hash method to each object, so that it can
self-summarize for the benefit of Region Report tool
---
modules/Bio/EnsEMBL/Gene.pm | 1 +
modules/Bio/EnsEMBL/Transcript.pm | 67 ++++++++++++++++++++----------
modules/Bio/EnsEMBL/Translation.pm | 23 ++++++++--
3 files changed, 65 insertions(+), 26 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 00691a6c03..2fd7ef8a3e 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -1484,6 +1484,7 @@ sub summary_as_hash {
$summary{'stable_id'} = $self->stable_id;
$summary{'description'} = $self->description;
$summary{'biotype'} = $self->biotype;
+ $summary{'strand'} = $self->strand;
return \%summary;
}
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 7aedfaa5ae..fe54e42227 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -47,8 +47,6 @@ A representation of a transcript within the Ensembl system. A transcript
consists of a set of Exons and (possibly) a Translation which defines the
coding and non-coding regions of the exons.
-=head1 METHODS
-
=cut
package Bio::EnsEMBL::Transcript;
@@ -752,7 +750,7 @@ sub translation {
Description: Fetches all alternative translations defined for this
transcript. The canonical translation is not returned.
- Returntype : Array reference to Bio::EnsEMBL::Translation
+ Returntype : Arrayref to Bio::EnsEMBL::Translation
Exceptions : None
Caller : General
Status : Stable
@@ -813,7 +811,7 @@ sub add_alternative_translation {
Example : none
Description: Retrieves all Exon sequences and concats them together.
No phase padding magic is done, even if phases do not align.
- Returntype : txt
+ Returntype : Text
Exceptions : none
Caller : general
Status : Stable
@@ -867,7 +865,7 @@ sub spliced_seq {
An empty string is returned if this transcript is a pseudogene
(i.e. is non-translateable).
- Returntype : txt
+ Returntype : Text
Exceptions : none
Caller : general
Status : Stable
@@ -1263,7 +1261,7 @@ sub add_Attributes {
Title : add_Exon
Usage : $trans->add_Exon($exon)
- Returns : Nothing
+ Returns : None
Args [1]: Bio::EnsEMBL::Exon object to add
Args [2]: rank
Exceptions: throws if not a valid Bio::EnsEMBL::Exon
@@ -1401,7 +1399,7 @@ sub add_Exon {
constitutive exons if the CONSTITUTIVE argument is
true.
- Returntype : a list reference to Bio::EnsEMBL::Exon objects
+ Returntype : listref to Bio::EnsEMBL::Exon objects
Exceptions : none
Caller : general
Status : Stable
@@ -1448,7 +1446,7 @@ sub get_all_Exons {
transcript in order, i.e. the first exon in the
listref is the 5prime most exon in the transcript.
- Returntype : a list reference to Bio::EnsEMBL::Exon objects
+ Returntype : listref to Bio::EnsEMBL::Exon objects
Exceptions : none
Caller : general
Status : Stable
@@ -1467,7 +1465,7 @@ sub get_all_constitutive_Exons {
Description: Returns an listref of the introns in this transcript in order.
i.e. the first intron in the listref is the 5prime most exon in
the transcript.
- Returntype : a list reference to Bio::EnsEMBL::Intron objects
+ Returntype : listref to Bio::EnsEMBL::Intron objects
Exceptions : none
Caller : general
Status : Stable
@@ -1883,11 +1881,12 @@ sub get_TranscriptMapper {
=head2 start_Exon
- Title : start_Exon
- Usage : $start_exon = $transcript->start_Exon;
- Returns : The first exon in the transcript.
- Args : NONE
- Status : Stable
+ Title : start_Exon
+ Usage : $start_exon = $transcript->start_Exon;
+ Returntype : Bio::EnsEMBL::Exon
+ Description : The first exon in the transcript.
+ Args : NONE
+ Status : Stable
=cut
@@ -1899,11 +1898,12 @@ sub start_Exon {
=head2 end_Exon
- Title : end_exon
- Usage : $end_exon = $transcript->end_Exon;
- Returns : The last exon in the transcript.
- Args : NONE
- Status : Stable
+ Title : end_exon
+ Usage : $end_exon = $transcript->end_Exon;
+ Description : The last exon in the transcript.
+ Returntype : Bio::EnsEMBL::Exon
+ Args : NONE
+ Status : Stable
=cut
@@ -1918,7 +1918,7 @@ sub end_Exon {
Title : description
Usage : $obj->description($newval)
Function:
- Returns : value of description
+ Returns : String
Args : newvalue (optional)
Status : Stable
@@ -1936,7 +1936,7 @@ sub description {
Title : version
Usage : $obj->version()
Function:
- Returns : value of version
+ Returns : String
Args :
Status : Stable
@@ -1954,7 +1954,7 @@ sub version {
Title : stable_id
Usage : $obj->stable_id
Function:
- Returns : value of stable_id
+ Returns : String
Args :
Status : Stable
@@ -2612,7 +2612,7 @@ sub _compare_xrefs {
lazy-loaded. It will also call the equivalent
method on any translation and on all exons of the
transcript.
- Returns : Nothing.
+ Returntype : None
=cut
@@ -2649,6 +2649,27 @@ sub load {
} ## end sub load
+=head2 summary_as_hash
+
+ Example : $transcript_summary = $transcript->summary_as_hash();
+ Description : Retrieves a textual summary of this Transcript object.
+ Returns : hashref of descriptive strings
+
+=cut
+
+sub summary_as_hash {
+ my $self = shift;
+ my %summary;
+ $summary{'stable_id'} = $self->stable_id;
+ $summary{'description'} = $self->description;
+ $summary{'biotype'} = $self->biotype;
+ $summary{'start'} = $self->start;
+ $summary{'end'} = $self->end;
+ $summary{'strand'} = $self->strand;
+ $summary{'display_id'} = $self->display_id;
+ return \%summary;
+}
+
###########################
# DEPRECATED METHODS FOLLOW
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index 4eba7819fa..bdf2d5ee51 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -526,7 +526,7 @@ sub modified_date {
a hash that maps old to new exons for a whole gene
Description: maps start end end exon according to mapping table.
If an exon is not mapped, just keep the old one.
- Returntype: none
+ Returntype : none
Exceptions : none
Caller : Transcript->transform()
Status : Stable
@@ -1122,7 +1122,7 @@ sub modify_translation {
an object needs to be fully loaded. This method
loads the parts of the object that are usually
lazy-loaded.
- Returns : Nothing.
+ Returns : none
=cut
@@ -1161,7 +1161,7 @@ sub temporary_id {
=head2 get_all_DASFactories
Function : Retrieves a listref of registered DAS objects
- Returntype: DAS objects
+ Returntype: Listref of DAS Objects
Exceptions: none
Caller : webcode
Example : $dasref = $prot->get_all_DASFactories;
@@ -1201,5 +1201,22 @@ sub get_all_DAS_Features{
return $self->SUPER::get_all_DAS_Features($slice);
}
+=head2 summary_as_hash
+
+ Example : $gene_summary = $gene->summary_as_hash();
+ Description : Retrieves a textual summary of this Gene object.
+ Returns : hashref of descriptive strings
+
+=cut
+
+sub summary_as_hash {
+ my $self = shift;
+ my %summary;
+ $summary{'stable_id'} = $self->stable_id;
+ $summary{'display_id'} = $self->display_id;
+ $summary{'genomic_start'} = $self->genomic_start;
+ $summary{'genomic_end'} = $self->genomic_end;
+ return \%summary;
+}
1;
--
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