Commit 188692f6 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Streamline LICENSE, CONTACT, and AUTHOR sections in POD.

Formatting of SYNOPSIS code.

Passes unit tests.
parent 2edc352e
#
# Ensembl module for Bio::EnsEMBL::AffyArray
#
# You may distribute this module under the same terms as Perl itself
=head1 LICENSE
=head1 NAME
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
Bio::EnsEMBL::AffyArray - A module to represent an Affymetrix array.
This software is distributed under a modified Apache license.
For license details, please see
=head1 SYNOPSIS
http://www.ensembl.org/info/about/code_licence.html
use Bio::EnsEMBL::AffyArray;
=head1 CONTACT
my $array = Bio::EnsEMBL::AffyArray->new(
-NAME => 'Affy-1',
-INCLUDED_IN => $another_array,
-SETSIZE => 16,
);
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
=head1 DESCRIPTION
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
An AffyArray object represents an Affymetrix array. The data (currently the
name, probeset size and parent array) are stored in the oligo_array table.
=cut
Each array can have a parent array (another array that contains all the probes
of this array). This is rarely (if ever) used.
=head1 NAME
=head1 AUTHOR
Bio::EnsEMBL::AffyArray - A module to represent an Affymetrix array.
This module was originally written by Arne Stabenau, but was changed to be a
subclass of OligoArray by Ian Sealy.
=head1 SYNOPSIS
This module is part of the Ensembl project: http://www.ensembl.org/
use Bio::EnsEMBL::AffyArray;
=head1 CONTACT
my $array = Bio::EnsEMBL::AffyArray->new(
-NAME => 'Affy-1',
-INCLUDED_IN => $another_array,
-SETSIZE => 16,
);
=head1 DESCRIPTION
An AffyArray object represents an Affymetrix array. The data (currently
the name, probeset size and parent array) are stored in the oligo_array
table.
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
Each array can have a parent array (another array that contains all the
probes of this array). This is rarely (if ever) used.
=head1 METHODS
......
#
# Ensembl module for Bio::EnsEMBL::AffyFeature
#
# You may distribute this module under the same terms as Perl itself
=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
......@@ -10,33 +25,22 @@ mapping.
=head1 SYNOPSIS
use Bio::EnsEMBL::AffyFeature;
use Bio::EnsEMBL::AffyFeature;
my $feature = Bio::EnsEMBL::AffyFeature->new(
-PROBE => $probe,
-MISMATCHCOUNT => 0,
-SLICE => $chr_1_slice,
-START => 1_000_000,
-END => 1_000_024,
-STRAND => -1,
);
my $feature = Bio::EnsEMBL::AffyFeature->new(
-PROBE => $probe,
-MISMATCHCOUNT => 0,
-SLICE => $chr_1_slice,
-START => 1_000_000,
-END => 1_000_024,
-STRAND => -1,
);
=head1 DESCRIPTION
An AffyFeature object represents the genomic placement of an AffyProbe
object. The data are stored in the oligo_feature table.
=head1 AUTHOR
This module was originally written by Arne Stabenau, but was changed to be a
subclass of OligoArray by Ian Sealy.
This module is part of the Ensembl project: http://www.ensembl.org/
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
......
#
# Ensembl module for Bio::EnsEMBL::AffyProbe
#
# You may distribute this module under the same terms as Perl itself
=head1 LICENSE
=head1 NAME
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
Bio::EnsEMBL::AffyProbe - A module to represent an Affymetrix probe.
This software is distributed under a modified Apache license.
For license details, please see
=head1 SYNOPSIS
http://www.ensembl.org/info/about/code_licence.html
use Bio::EnsEMBL::OligoProbe;
=head1 CONTACT
my $probe = Bio::EnsEMBL::OligoProbe->new(
-PROBENAME => 'Probe-1',
-ARRAY => $array,
-PROBESET => 'Probeset-1',
);
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
=head1 DESCRIPTION
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
An AffyProbe object represents an Affy probe on a microarray. The data
(currently the name, array, length, probeset and description) are stored in the
oligo_probe table. The complete name of a probe is the concatenation of the
array name, the probeset and the probe name.
=cut
For Affy arrays, a probe can be part of more than one array, but only part of
one probeset. On each Affy array the probe has a slightly different name. For
example, two different complete names for the same probe might be
DrosGenome1:AFFX-LysX-5_at:535:35; and Drosophila_2:AFFX-LysX-5_at:460:51;. In
the database, these two probes will have the same oligo_probe_id. Thus the same
Affy probe can have a number of different names and complete names depending on
which array it's on.
=head1 NAME
Bio::EnsEMBL::AffyProbe - A module to represent an Affymetrix probe.
=head1 AUTHOR
=head1 SYNOPSIS
This module was originally written by Arne Stabenau, but was changed to be a
subclass of OligoArray by Ian Sealy.
use Bio::EnsEMBL::OligoProbe;
This module is part of the Ensembl project: http://www.ensembl.org/
my $probe = Bio::EnsEMBL::OligoProbe->new(
-PROBENAME => 'Probe-1',
-ARRAY => $array,
-PROBESET => 'Probeset-1',
);
=head1 CONTACT
=head1 DESCRIPTION
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
An AffyProbe object represents an Affy probe on a microarray. The
data (currently the name, array, length, probeset and description) are
stored in the oligo_probe table. The complete name of a probe is the
concatenation of the array name, the probeset and the probe name.
For Affy arrays, a probe can be part of more than one array, but
only part of one probeset. On each Affy array the probe has a
slightly different name. For example, two different complete names
for the same probe might be DrosGenome1:AFFX-LysX-5_at:535:35; and
Drosophila_2:AFFX-LysX-5_at:460:51;. In the database, these two probes
will have the same oligo_probe_id. Thus the same Affy probe can have a
number of different names and complete names depending on which array
it's on.
=head1 METHODS
......
#
# Ensembl module for Bio::EnsEMBL::AlignStrainSlice
#
#
# Copyright Team Ensembl
#
# You may distribute this module under the same terms as perl itself
=head1 LICENSE
# POD documentation - main docs before the code
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
......@@ -14,39 +24,37 @@ Bio::EnsEMBL::AlignStrainSlice - Represents the slice of the genome aligned with
=head1 SYNOPSIS
$sa = $db->get_SliceAdaptor;
$sa = $db->get_SliceAdaptor;
$slice = $sa->fetch_by_region('chromosome', 'X', 1_000_000, 2_000_000);
$slice =
$sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );
$strainSlice1 = $slice->get_by_Strain($strain_name1);
$strainSlice2 = $slice->get_by_Strain($strain_name2);
$strainSlice1 = $slice->get_by_Strain($strain_name1);
$strainSlice2 = $slice->get_by_Strain($strain_name2);
my @strainSlices;
push @strainSlices, $strainSlice1;
push @strainSlices, $strainSlice2;
my @strainSlices;
push @strainSlices, $strainSlice1;
push @strainSlices, $strainSlice2;
$alignSlice = Bio::EnsEMBL::AlignStrainSlice->new(-SLICE => $slice,
-STRAINS => \@strainSlices);
$alignSlice = Bio::EnsEMBL::AlignStrainSlice->new(
-SLICE => $slice,
-STRAINS => \@strainSlices
);
#get coordinates of variation in alignSlice
my $alleleFeatures = $strainSlice1->get_all_AlleleFeature_Slice();
foreach my $af (@{$alleleFeatures}){
my $new_feature = $alignSlice->alignFeature($af, $strainSlice1);
print "Coordinates of the feature in AlignSlice are: ", $new_feature->start, "-", $new_feature->end, "\n";
}
# Get coordinates of variation in alignSlice
my $alleleFeatures = $strainSlice1->get_all_AlleleFeature_Slice();
foreach my $af ( @{$alleleFeatures} ) {
my $new_feature = $alignSlice->alignFeature( $af, $strainSlice1 );
print( "Coordinates of the feature in AlignSlice are: ",
$new_feature->start, "-", $new_feature->end, "\n" );
}
=head1 DESCRIPTION
A AlignStrainSlice object represents a region of a genome align for certain strains. It can be used to align
certain strains to a reference slice
=head1 CONTACT
This modules is part of the Ensembl project http://www.ensembl.org
Questions can be posted to the ensembl-dev mailing list:
ensembl-dev@ebi.ac.uk
A AlignStrainSlice object represents a region of a genome align for
certain strains. It can be used to align certain strains to a reference
slice.
=head1 METHODS
......
#
# Object for storing sequence analysis details
#
# Cared for by Michele Clamp <michele@sanger.ac.uk>
#
# Copyright Michele Clamp
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
......@@ -17,34 +24,30 @@ Bio::EnsEMBL::Analysis.pm - Stores details of an analysis run
=head1 SYNOPSIS
my $obj = new Bio::EnsEMBL::Analysis(
-id => $id,
-logic_name => 'SWIRBlast',
-db => $db,
-db_version => $db_version,
-db_file => $db_file,
-program => $program,
-program_version => $program_version,
-program_file => $program_file,
-gff_source => $gff_source,
-gff_feature => $gff_feature,
-module => $module,
-module_version => $module_version,
-parameters => $parameters,
-created => $created,
-description => 'some warm words about this analysis',
-display_label => 'UNIprot alignment',
-displayable => '1',
-web_data => 'web metadata info'
);
my $obj = new Bio::EnsEMBL::Analysis(
-id => $id,
-logic_name => 'SWIRBlast',
-db => $db,
-db_version => $db_version,
-db_file => $db_file,
-program => $program,
-program_version => $program_version,
-program_file => $program_file,
-gff_source => $gff_source,
-gff_feature => $gff_feature,
-module => $module,
-module_version => $module_version,
-parameters => $parameters,
-created => $created,
-description => 'some warm words about this analysis',
-display_label => 'UNIprot alignment',
-displayable => '1',
-web_data => 'web metadata info'
);
=head1 DESCRIPTION
Object to store details of an analysis run
=head1 CONTACT
Post questions to the EnsEMBL dev mailing list: <ensembl-dev@ebi.ac.uk>
Object to store details of an analysis run.
=head1 METHODS
......
#
# BioPerl module for PairAlign object
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
# POD documentation - main docs before the code
......@@ -22,41 +33,33 @@ Give standard usage here
Contains list of sub alignments making up a dna-dna alignment
Creation:
my $pair = new Bio::EnsEMBL::FeaturePair(-start => $qstart,
-end => $qend,
-strand => $qstrand,
-hstart => $hstart,
-hend => $hend,
-hend => $hstrand,
);
my $pairaln = new Bio::EnsEMBL::Analysis::PairAlign;
$pairaln->addFeaturePair($pair);
my $pair = new Bio::EnsEMBL::FeaturePair(
-start => $qstart,
-end => $qend,
-strand => $qstrand,
-hstart => $hstart,
-hend => $hend,
-hend => $hstrand,
);
my $pairaln = new Bio::EnsEMBL::Analysis::PairAlign;
$pairaln->addFeaturePair($pair);
Any number of pair alignments can be added to the PairAlign object
Manipulation:
To convert between coordinates :
my $cdna_coord = $pair->genomic2cDNA($gen_coord);
my $gen_coord = $pair->cDNA2genomic($cdna_coord);
=head1 CONTACT
Describe contact details here
To convert between coordinates:
=head1 APPENDIX
my $cdna_coord = $pair->genomic2cDNA($gen_coord);
my $gen_coord = $pair->cDNA2genomic($cdna_coord);
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=head1 METHODS
=cut
# Let the code begin...
package Bio::EnsEMBL::Analysis::PairAlign;
use vars qw(@ISA);
......
=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
package Bio::EnsEMBL::Analysis::Programs;
use strict;
......
package Bio::EnsEMBL::ArchiveStableId;
=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
......@@ -6,11 +24,10 @@ Bio::EnsEMBL::ArchiveStableId
=head1 SYNOPSIS
=head1 DESCRIPTION
ArchiveStableId objects are the main workunit for retrieving stable id archived
information from EnsEMBL core database.
ArchiveStableId objects are the main workunit for retrieving stable id
archived information from EnsEMBL core database.
Attributes:
type: Gene, Transcript, Translation, Exon, other, undef
......@@ -55,23 +72,9 @@ Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Bio::EnsEMBL::StableIdEvent
Bio::EnsEMBL::StableIdHistoryTree
=head1 LICENCE
This code is distributed under an Apache style licence:
Please see http://www.ensembl.org/code_licence.html for details
=head1 AUTHOR
Ensembl core API team
Currently maintained by Patrick Meidl <meidl@ebi.ac.uk>
=head1 CONTACT
Please post comments/questions to the Ensembl development list
<ensembl-dev@ebi.ac.uk>
=cut
package Bio::EnsEMBL::ArchiveStableId;
use strict;
use warnings;
......
#
# Ensembl module for Bio::EnsEMBL::AssemblyExceptionFeature
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
=head1 LICENSE
# POD documentation - main docs before the code
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
=head1 NAME
This software is distributed under a modified Apache license.
For license details, please see
Bio::EnsEMBL::AssemblyExceptionFeature - A feature that represents an assembly exception
http://www.ensembl.org/info/about/code_licence.html
=head1 SYNOPSIS
=head1 CONTACT
use Bio::EnsEMBL::AssemblyExceptionFeature;
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
$feature = Bio::EnsEMBL::AssemblyExceptionFeature->new(-start => 100,
-end => 220,
-type => 'HAP',
-slice => $slice,
-adaptor => $adaptor);
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=head1 DESCRIPTION
=cut
=head1 NAME
Certain features, e.g. Haplotypes and PARs, are represented as "exceptions" to the
normal assembly. This class represents such features.
Bio::EnsEMBL::AssemblyExceptionFeature - A feature that represents an assembly exception
=head1 AUTHOR - Glenn Proctor
=head1 SYNOPSIS