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Bio::DB::GFF::Feature 1.4
Bio::DB::GFF::Feature is a relative segment identified by a feature type. more>>
Bio::DB::GFF::Feature is a relative segment identified by a feature type.
Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too, if needed).
Bio::DB::GFF::Feature adds new methods to retrieve the annotations type, group, and other GFF attributes. Annotation types are represented by Bio::DB::GFF::Typename objects, a simple class that has two methods called method() and source(). These correspond to the method and source fields of a GFF file.
Annotation groups serve the dual purpose of giving the annotation a human-readable name, and providing higher-order groupings of subfeatures into features. The groups returned by this module are objects of the Bio::DB::GFF::Featname class.
Bio::DB::GFF::Feature inherits from and implements the abstract methods of Bio::SeqFeatureI, allowing it to interoperate with other Bioperl modules.
Generally, you will not create or manipulate Bio::DB::GFF::Feature objects directly, but use those that are returned by the Bio::DB::GFF::RelSegment->features() method.
Important note about start() vs end()
If features are derived from segments that use relative addressing (which is the default), then start() will be less than end() if the feature is on the opposite strand from the reference sequence. This breaks Bio::SeqI compliance, but is necessary to avoid having the real genomic locations designated by start() and end() swap places when changing reference points.
To avoid this behavior, call $segment->absolute(1) before fetching features from it. This will force everything into absolute coordinates.
For example:
my $segment = $db->segment(CHROMOSOME_I);
$segment->absolute(1);
my @features = $segment->features(transcript);
<<lessBio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too, if needed).
Bio::DB::GFF::Feature adds new methods to retrieve the annotations type, group, and other GFF attributes. Annotation types are represented by Bio::DB::GFF::Typename objects, a simple class that has two methods called method() and source(). These correspond to the method and source fields of a GFF file.
Annotation groups serve the dual purpose of giving the annotation a human-readable name, and providing higher-order groupings of subfeatures into features. The groups returned by this module are objects of the Bio::DB::GFF::Featname class.
Bio::DB::GFF::Feature inherits from and implements the abstract methods of Bio::SeqFeatureI, allowing it to interoperate with other Bioperl modules.
Generally, you will not create or manipulate Bio::DB::GFF::Feature objects directly, but use those that are returned by the Bio::DB::GFF::RelSegment->features() method.
Important note about start() vs end()
If features are derived from segments that use relative addressing (which is the default), then start() will be less than end() if the feature is on the opposite strand from the reference sequence. This breaks Bio::SeqI compliance, but is necessary to avoid having the real genomic locations designated by start() and end() swap places when changing reference points.
To avoid this behavior, call $segment->absolute(1) before fetching features from it. This will force everything into absolute coordinates.
For example:
my $segment = $db->segment(CHROMOSOME_I);
$segment->absolute(1);
my @features = $segment->features(transcript);
Download (4.7MB)
Added: 2006-06-09 License: Perl Artistic License Price:
1232 downloads
Bio::Graphics::Feature 1.4
Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. more>>
Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel.
SYNOPSIS
use Bio::Graphics::Feature;
# create a simple feature with no internal structure
$f = Bio::Graphics::Feature->new(-start => 1000,
-stop => 2000,
-type => transcript,
-name => alpha-1 antitrypsin,
-desc => an enzyme inhibitor,
);
# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => ABC-3,
-type => gapped_alignment,
-subtype => similarity);
# build up a gene exon by exon
$e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>exon);
$e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>exon);
$e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>exon);
$f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>gene);
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.
<<lessSYNOPSIS
use Bio::Graphics::Feature;
# create a simple feature with no internal structure
$f = Bio::Graphics::Feature->new(-start => 1000,
-stop => 2000,
-type => transcript,
-name => alpha-1 antitrypsin,
-desc => an enzyme inhibitor,
);
# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => ABC-3,
-type => gapped_alignment,
-subtype => similarity);
# build up a gene exon by exon
$e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>exon);
$e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>exon);
$e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>exon);
$f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>gene);
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.
Download (4.7MB)
Added: 2006-10-21 License: Perl Artistic License Price:
1098 downloads
Bio::Graphics::FeatureFile 1.4
Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file. more>>
Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file.
SYNOPSIS
use Bio::Graphics::FeatureFile;
my $data = Bio::Graphics::FeatureFile->new(-file => features.txt);
# create a new panel and render contents of the file onto it
my $panel = $data->new_panel;
my $tracks_rendered = $data->render($panel);
# or do it all in one step
my ($tracks_rendered,$panel) = $data->render;
# for more control, render tracks individually
my @feature_types = $data->types;
for my $type (@feature_types) {
my $features = $data->features($type);
my %options = $data->style($type);
$panel->add_track($features,%options); # assuming we have a Bio::Graphics::Panel
}
# get individual settings
my $est_fg_color = $data->setting(EST => fgcolor);
# or create the FeatureFile by hand
# add a type
$data->add_type(EST => {fgcolor=>blue,height=>12});
# add a feature
my $feature = Bio::Graphics::Feature->new(
# params
); # or some other SeqI
$data->add_feature($feature=>EST);
The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you can interrogate it for its consistuent features and their settings, or render the entire file onto a Bio::Graphics::Panel.
This moduel is a precursor of Jason Stajichs Bio::Annotation::Collection class, and fulfills a similar function of storing a collection of sequence features. However, it also stores rendering information about the features, and does not currently follow the CollectionI interface.
<<lessSYNOPSIS
use Bio::Graphics::FeatureFile;
my $data = Bio::Graphics::FeatureFile->new(-file => features.txt);
# create a new panel and render contents of the file onto it
my $panel = $data->new_panel;
my $tracks_rendered = $data->render($panel);
# or do it all in one step
my ($tracks_rendered,$panel) = $data->render;
# for more control, render tracks individually
my @feature_types = $data->types;
for my $type (@feature_types) {
my $features = $data->features($type);
my %options = $data->style($type);
$panel->add_track($features,%options); # assuming we have a Bio::Graphics::Panel
}
# get individual settings
my $est_fg_color = $data->setting(EST => fgcolor);
# or create the FeatureFile by hand
# add a type
$data->add_type(EST => {fgcolor=>blue,height=>12});
# add a feature
my $feature = Bio::Graphics::Feature->new(
# params
); # or some other SeqI
$data->add_feature($feature=>EST);
The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you can interrogate it for its consistuent features and their settings, or render the entire file onto a Bio::Graphics::Panel.
This moduel is a precursor of Jason Stajichs Bio::Annotation::Collection class, and fulfills a similar function of storing a collection of sequence features. However, it also stores rendering information about the features, and does not currently follow the CollectionI interface.
Download (4.7MB)
Added: 2006-06-12 License: Perl Artistic License Price:
1229 downloads
Bio::Affymetrix::CDF 0.5
Bio::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files. more>>
Bio::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files.
SYNOPSIS
use Bio::Affymetrix::CDF;
# Parse the CDF file
my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0});
$cdf->parse_from_file("foo.cdf");
# Find some fun facts about this chip type
print $cdf->rows().",".$cdf->cols()."n";
print $cdf->version()."n";
# Print out all of the probeset names on this chip type
foreach my $i (keys %{$chp->probesets}) { print $chp->probesets->{$i}->name()."n"; }
The Affymetrix microarray system produces files in a variety of formats. If this means nothing to you, these modules are probably not for you :). This module parses CDF files. Use this module if you want to find out about the design of an Affymetrix GeneChip, or you need the object for another one of the modules in this package.
All of the Bio::Affymetrix modules parse a file entirely into memory. You therefore need enough memory to hold these objects. For some applications, parsing as a stream may be more appropriate- hopefully the source to these modules will give enough clues to make this an easy task. This module in particular takes a lot of memory if probe information is also stored (about 150Mb). Memory usage is not too onorous (about 15Mb) if probe level information is omitted. You can.control this by setting probemode=>1 or probemode=>0 in the constructor.
You can also use these modules to write CDF files (using the write_to_filehandle method). See COMPATIBILITY for some important caveats.
<<lessSYNOPSIS
use Bio::Affymetrix::CDF;
# Parse the CDF file
my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0});
$cdf->parse_from_file("foo.cdf");
# Find some fun facts about this chip type
print $cdf->rows().",".$cdf->cols()."n";
print $cdf->version()."n";
# Print out all of the probeset names on this chip type
foreach my $i (keys %{$chp->probesets}) { print $chp->probesets->{$i}->name()."n"; }
The Affymetrix microarray system produces files in a variety of formats. If this means nothing to you, these modules are probably not for you :). This module parses CDF files. Use this module if you want to find out about the design of an Affymetrix GeneChip, or you need the object for another one of the modules in this package.
All of the Bio::Affymetrix modules parse a file entirely into memory. You therefore need enough memory to hold these objects. For some applications, parsing as a stream may be more appropriate- hopefully the source to these modules will give enough clues to make this an easy task. This module in particular takes a lot of memory if probe information is also stored (about 150Mb). Memory usage is not too onorous (about 15Mb) if probe level information is omitted. You can.control this by setting probemode=>1 or probemode=>0 in the constructor.
You can also use these modules to write CDF files (using the write_to_filehandle method). See COMPATIBILITY for some important caveats.
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Added: 2007-03-06 License: Perl Artistic License Price:
963 downloads
Bio::Das::Lite 1.49
Bio::Das::Lite is a Perl extension for the DAS (HTTP+XML) Protocol. more>>
Bio::Das::Lite is a Perl extension for the DAS (HTTP+XML) Protocol.
SYNOPSIS
use Bio::Das::Lite;
my $bdl = Bio::Das::Lite->new_from_registry({category => Chromosome});
my $results = $bdl->features(22);
SUBROUTINES/METHODS
new : Constructor
my $das = Bio::Das::Lite->new(http://das.ensembl.org/das/ensembl1834);
my $das = Bio::Das::Lite->new({
timeout => 60,
dsn => http://user:pass@das.ensembl.org/das/ensembl1834,
http_proxy => http://user:pass@webcache.local.com:3128/,
});
Options can be: dsn (optional scalar or array ref, URLs of DAS services)
timeout (optional int, HTTP fetch timeout in seconds)
http_proxy (optional scalar, web cache or proxy if not set in %ENV)
caching (optional bool, primitive caching on/off)
callback (optional code ref, callback for processed XML blocks)
registry (optional array ref containing DAS registry service URLs
defaults to http://das.sanger.ac.uk/registry/services/das)
proxy_user (optional scalar, username for authenticating forward-proxy)
proxy_pass (optional scalar, password for authenticating forward-proxy)
user_agent (optional scalar, User-Agent HTTP request header value)
new_from_registry : Constructor
Similar to new above but supports capabilities and category
in the given hashref, using them to query the DAS registry and
configuring the DSNs accordingly.
my $das = Bio::Das::Lite->new_from_registry({
capabilities => [features],
category => [Protein Sequence],
});
Options are as above, plus
capability (optional arrayref of capabilities)
category (optional arrayref of categories)
<<lessSYNOPSIS
use Bio::Das::Lite;
my $bdl = Bio::Das::Lite->new_from_registry({category => Chromosome});
my $results = $bdl->features(22);
SUBROUTINES/METHODS
new : Constructor
my $das = Bio::Das::Lite->new(http://das.ensembl.org/das/ensembl1834);
my $das = Bio::Das::Lite->new({
timeout => 60,
dsn => http://user:pass@das.ensembl.org/das/ensembl1834,
http_proxy => http://user:pass@webcache.local.com:3128/,
});
Options can be: dsn (optional scalar or array ref, URLs of DAS services)
timeout (optional int, HTTP fetch timeout in seconds)
http_proxy (optional scalar, web cache or proxy if not set in %ENV)
caching (optional bool, primitive caching on/off)
callback (optional code ref, callback for processed XML blocks)
registry (optional array ref containing DAS registry service URLs
defaults to http://das.sanger.ac.uk/registry/services/das)
proxy_user (optional scalar, username for authenticating forward-proxy)
proxy_pass (optional scalar, password for authenticating forward-proxy)
user_agent (optional scalar, User-Agent HTTP request header value)
new_from_registry : Constructor
Similar to new above but supports capabilities and category
in the given hashref, using them to query the DAS registry and
configuring the DSNs accordingly.
my $das = Bio::Das::Lite->new_from_registry({
capabilities => [features],
category => [Protein Sequence],
});
Options are as above, plus
capability (optional arrayref of capabilities)
category (optional arrayref of categories)
Download (0.032MB)
Added: 2007-03-20 License: Perl Artistic License Price:
949 downloads
Bio::DB::Flat::BDB::swissprot 1.4
Bio::DB::Flat::BDB::swissprot is a swissprot adaptor for Open-bio standard BDB-indexed flat file. more>>
Bio::DB::Flat::BDB::swissprot is a swissprot adaptor for Open-bio standard BDB-indexed flat file.
SYNOPSIS
See Bio::DB::Flat.
This module allows swissprot files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat.
<<lessSYNOPSIS
See Bio::DB::Flat.
This module allows swissprot files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat.
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Added: 2006-10-11 License: Perl Artistic License Price:
1111 downloads
DB Designer Fork 1.3
DB Designer Fork is a fork of the fabFORCE DBDesigner 4. more>>
DB Designer Fork is a fork of the fabFORCE DBDesigner 4. DBDesigner is a visual database design system that integrates entity relationship design and database creation.
The project generates SQL scripts for Oracle, SQL Server, MySQL, and FireBird.
<<lessThe project generates SQL scripts for Oracle, SQL Server, MySQL, and FireBird.
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Added: 2007-05-11 License: GPL (GNU General Public License) Price:
923 downloads
Bio::Genex::Software 2.6.0
Bio::Genex::Software is Perl module with methods for processing data from the GeneX DB table: Software. more>>
Bio::Genex::Software is Perl module with methods for processing data from the GeneX DB table: Software.
SYNOPSIS
use Bio::Genex::Software;
# instantiating an instance
my $Software = Bio::Genex::Software->new(id=>47);
# retrieve data from the DB for all columns
$Software->fetch();
# creating an instance, without pre-fetching all columns
my $Software = new Bio::Genex::Software(id=>47);
# creating an instance with pre-fetched data
my $Software = new Bio::Genex::Software(id=>47, fetch_all=>1);
# retrieving multiple instances via primary keys
my @objects = Bio::Genex::Software->get_objects(23,57,98)
# retrieving all instances from a table
my @objects = Bio::Genex::Software->get_all_objects();
# retrieving the primary key for an object, generically
my $primary_key = $Software->id();
# or specifically
my $sw_pk_val = $Software->sw_pk();
# retreving other DB column attributes
my $name_val = $Software->name();
$Software->name($value);
my $version_val = $Software->version();
$Software->version($value);
my $type_val = $Software->type();
$Software->type($value);
my $con_fk_val = $Software->con_fk();
$Software->con_fk($value);
Each Genex class has a one to one correspondence with a GeneX DB table of the same name (i.e. the corresponding table for Bio::Genex::Software is Software).
Most applications will first create an instance of Bio::Genex::Software and then fetch the data for the object from the DB by invoking fetch().
However, in cases where you may only be accessing a single value from an object the built-in delayed fetch mechanism can be used. All objects are created without pre-fetching any data from the DB. Whenever an attribute of the object is accessed via a getter method, the data for that attribute will be fetched from the DB if it has not already been. Delayed fetching happens transparently without the user needing to enable or disable any features.
Since data is not be fetched from the DB until it is accessed by the calling application, it could presumably save a lot of access time for large complicated objects when only a few attribute values are needed.
<<lessSYNOPSIS
use Bio::Genex::Software;
# instantiating an instance
my $Software = Bio::Genex::Software->new(id=>47);
# retrieve data from the DB for all columns
$Software->fetch();
# creating an instance, without pre-fetching all columns
my $Software = new Bio::Genex::Software(id=>47);
# creating an instance with pre-fetched data
my $Software = new Bio::Genex::Software(id=>47, fetch_all=>1);
# retrieving multiple instances via primary keys
my @objects = Bio::Genex::Software->get_objects(23,57,98)
# retrieving all instances from a table
my @objects = Bio::Genex::Software->get_all_objects();
# retrieving the primary key for an object, generically
my $primary_key = $Software->id();
# or specifically
my $sw_pk_val = $Software->sw_pk();
# retreving other DB column attributes
my $name_val = $Software->name();
$Software->name($value);
my $version_val = $Software->version();
$Software->version($value);
my $type_val = $Software->type();
$Software->type($value);
my $con_fk_val = $Software->con_fk();
$Software->con_fk($value);
Each Genex class has a one to one correspondence with a GeneX DB table of the same name (i.e. the corresponding table for Bio::Genex::Software is Software).
Most applications will first create an instance of Bio::Genex::Software and then fetch the data for the object from the DB by invoking fetch().
However, in cases where you may only be accessing a single value from an object the built-in delayed fetch mechanism can be used. All objects are created without pre-fetching any data from the DB. Whenever an attribute of the object is accessed via a getter method, the data for that attribute will be fetched from the DB if it has not already been. Delayed fetching happens transparently without the user needing to enable or disable any features.
Since data is not be fetched from the DB until it is accessed by the calling application, it could presumably save a lot of access time for large complicated objects when only a few attribute values are needed.
Download (0.54MB)
Added: 2007-01-08 License: Perl Artistic License Price:
1022 downloads
Bio::Index::Blast 1.4
Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s). more>>
Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s).
SYNOPSIS
use strict;
use Bio::Index::Blast;
my ($indexfile,$file1, $file2);
my $index = new Bio::Index::Blast(-filename => $indexfile,
-write_flag => 1);
$index->make_index($file1, $file2);
my $id;
my $data = $index->get_stream($id);
my $bplite_report = $index->fetch_report($id);
print "query is ", $bplite_report->query, "n";
while( my $sbjct = $bplite_report->nextSbjct ) {
print $sbjct->name, "n";
while( my $hsp = $sbjct->nextHSP ) {
print "t e-value ", $hsp->P,
}
print "n";
}
This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. Note: for best results use strict.
<<lessSYNOPSIS
use strict;
use Bio::Index::Blast;
my ($indexfile,$file1, $file2);
my $index = new Bio::Index::Blast(-filename => $indexfile,
-write_flag => 1);
$index->make_index($file1, $file2);
my $id;
my $data = $index->get_stream($id);
my $bplite_report = $index->fetch_report($id);
print "query is ", $bplite_report->query, "n";
while( my $sbjct = $bplite_report->nextSbjct ) {
print $sbjct->name, "n";
while( my $hsp = $sbjct->nextHSP ) {
print "t e-value ", $hsp->P,
}
print "n";
}
This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. Note: for best results use strict.
Download (4.7MB)
Added: 2006-10-10 License: Perl Artistic License Price:
1111 downloads
Bio::Biblio::Patent 1.4
Bio::Biblio::Patent is a representation of a patent. more>>
Bio::Biblio::Patent is a representation of a patent.
SYNOPSIS
$obj = new Bio::Biblio::Patent (-doc_number => 1-2-3-4-5);
#--- OR ---
$obj = new Bio::Biblio::Patent;
$obj->doc_number (1-2-3-4-5);
A storage object for a patent. See its place in the class hierarchy in
http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
Attributes
The following attributes are specific to this class (however, you can also set and get all attributes defined in the parent classes):
doc_number
doc_office
doc_type
applicants type: array ref of Bio::Biblio::Providers
<<lessSYNOPSIS
$obj = new Bio::Biblio::Patent (-doc_number => 1-2-3-4-5);
#--- OR ---
$obj = new Bio::Biblio::Patent;
$obj->doc_number (1-2-3-4-5);
A storage object for a patent. See its place in the class hierarchy in
http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
Attributes
The following attributes are specific to this class (however, you can also set and get all attributes defined in the parent classes):
doc_number
doc_office
doc_type
applicants type: array ref of Bio::Biblio::Providers
Download (4.7MB)
Added: 2006-10-11 License: Perl Artistic License Price:
1109 downloads
Bio::Tree::Tree 1.4
Bio::Tree::Tree is an Implementation of TreeI interface. more>>
Bio::Tree::Tree is an implementation of TreeI interface.
SYNOPSIS
# like from a TreeIO
my $treeio = new Bio::TreeIO(-format => newick, -file => treefile.dnd);
my $tree = $treeio->next_tree;
my @nodes = $tree->get_nodes;
my $root = $tree->get_root_node;
This object holds handles to Nodes which make up a tree.
<<lessSYNOPSIS
# like from a TreeIO
my $treeio = new Bio::TreeIO(-format => newick, -file => treefile.dnd);
my $tree = $treeio->next_tree;
my @nodes = $tree->get_nodes;
my $root = $tree->get_root_node;
This object holds handles to Nodes which make up a tree.
Download (4.7MB)
Added: 2006-10-10 License: Perl Artistic License Price:
1110 downloads
Bio::GMOD 0.28
Bio::GMOD is a unified API for Model Organism Databases. more>>
Bio::GMOD is a unified API for Model Organism Databases.
SYNOPSIS
Check the installed version of a MOD
use Bio::GMOD::Util::CheckVersions.pm
my $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase);
my $version = $mod->live_version;
Update a MOD installation
use Bio::GMOD::Update;
my $mod = Bio::GMOD::Update->new(-mod=>WormBase);
$gmod->update();
Fetch a list of genes from a MOD
use Bio::GMOD::Query;
my $mod = Bio::GMOD::Query->new(-mod=>WormBase);
my @genes = $mod->fetch(-class=>Gene,-name=>unc-26);
Bio::GMOD is a unified API for accessing various Model Organism Databases. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN.
MODs are highly curated resources of biological data. Although they typically incorporate sequence data housed at community repositories such as NCBI, they place this information within a framework of biological fuction gelaned from the published literature of experiments in model organisms.
Given the great proliferation of MODs, cross-site data mining strategies have been difficult to implement. Such strategies typically require a familiarity with both the underlying data model and the historical vocabulary of the model system.
Furthermore, the quickly-evolving nature of these projects have made installing a MOD locally and keeping it up-to-date a delicate and time-consuming experience.
<<lessSYNOPSIS
Check the installed version of a MOD
use Bio::GMOD::Util::CheckVersions.pm
my $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase);
my $version = $mod->live_version;
Update a MOD installation
use Bio::GMOD::Update;
my $mod = Bio::GMOD::Update->new(-mod=>WormBase);
$gmod->update();
Fetch a list of genes from a MOD
use Bio::GMOD::Query;
my $mod = Bio::GMOD::Query->new(-mod=>WormBase);
my @genes = $mod->fetch(-class=>Gene,-name=>unc-26);
Bio::GMOD is a unified API for accessing various Model Organism Databases. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN.
MODs are highly curated resources of biological data. Although they typically incorporate sequence data housed at community repositories such as NCBI, they place this information within a framework of biological fuction gelaned from the published literature of experiments in model organisms.
Given the great proliferation of MODs, cross-site data mining strategies have been difficult to implement. Such strategies typically require a familiarity with both the underlying data model and the historical vocabulary of the model system.
Furthermore, the quickly-evolving nature of these projects have made installing a MOD locally and keeping it up-to-date a delicate and time-consuming experience.
Download (0.070MB)
Added: 2006-10-10 License: Perl Artistic License Price:
1137 downloads
Bio::NEXUS::TreesBlock 0.67
Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file. more>>
Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file.
SYNOPSIS
if ( $type =~ /trees/i ) {
$block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose );
}
If a NEXUS block is a Trees Block, this module parses the block and stores the tree data.
METHODS
new
Title : new
Usage : block_object = new Bio::NEXUS::TreesBlock($block_type, $commands, $verbose );
Function: Creates a new Bio::NEXUS::TreesBlock object and automatically reads the file
Returns : Bio::NEXUS::TreesBlock object
Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1; optional)
clone
Title : clone
Usage : my $newblock = $block->clone();
Function: clone a block object (shallow)
Returns : Block object
Args : none
set_trees
Title : set_trees
Usage : $block->set_trees($trees);
Function: Sets the list of trees (Bio::NEXUS::Tree objects)
Returns : none
Args : ref to array of Bio::NEXUS::Tree objects
add_tree
Title : add_tree
Usage : $block->add_tree($tree);
Function: Add trees (Bio::NEXUS::Tree object)
Returns : none
Args : a Bio::NEXUS::Tree object
add_tree_from_newick
Title : add_tree_from_newick
Usage : $block->add_tree_from_newick($newick_tree, $tree_name);
Function: Add a tree (Bio::NEXUS::Tree object)
Returns : none
Args : a tree string in newick format and a name for the tree (scalars)
get_trees
Title : get_trees
Usage : $block->get_trees();
Function: Gets the list of trees (Bio::NEXUS::Tree objects) and returns it
Returns : ref to array of Bio::NEXUS::Tree objects
Args : none
get_tree
Title : get_tree
Usage : $block->get_tree($treename);
Function: Gets the first tree (Bio::NEXUS::Tree object) that matches the name given or the first tree if $treename is not specified. If no tree matches, returns undef.
Returns : a Bio::NEXUS::Tree object
Args : tree name or none
set_translate
Title : set_translate
Usage : $block->set_translate($translate);
Function: Sets the hash of translates for nodes names
Returns : none
Args : hash of translates
translate
Title : translate
Usage : $self->translate($num);
Function: Translates a number with its associated name.
Returns : integer or string
Args : integer
Method : Returns the name associated with that numbers translated name.
If it cant find an association, returns the number.
reroot_tree
Title : reroot_tree
Usage : $block->reroot_tree($outgroup,$root_position, $treename);
Function: Reroot a tree using an OTU as new outgroup.
Returns : none
Args : outgroup name, the distance before the root position and tree name
reroot_all_trees
Title : reroot_all_trees
Usage : $block->reroot_all_trees($outgroup, $root_position);
Function: Reroot all the trees in the treesblock tree. use an OTU as new outgroup
Returns : none
Args : outgroup name and root position
rename_otus
Title : rename_otus
Usage : $block->rename_otus(%translation);
Function: Renames nodes based on a translation hash
Returns : none
Args : hash containing translation (e.g., { old_name => new_name} )
Comments: nodes not included in translation hash are unaffected
select_otus
Name : select_otus
Usage : $nexus->select_otus(@otunames);
Function: select a subset of OTUs
Returns : a new nexus object
Args : a ref to array of OTU names
select_tree
Name : select_tree
Usage : $nexus->select_tree($treename);
Function: select a tree
Returns : a new nexus object
Args : a tree name
select_subtree
Name : select_subtree
Usage : $nexus->select_subtree($inodename);
Function: select a subtree
Returns : a new nexus object
Args : an internal node name for subtree to be selected
exclude_subtree
Name : exclude_subtree
Usage : $nexus->exclude_subtree($inodename);
Function: remove a subtree
Returns : a new nexus object
Args : an internal node for subtree to be removed
equals
Name : equals
Usage : $nexus->equals($another);
Function: compare if two NEXUS objects are equal
Returns : boolean
Args : a NEXUS object
<<lessSYNOPSIS
if ( $type =~ /trees/i ) {
$block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose );
}
If a NEXUS block is a Trees Block, this module parses the block and stores the tree data.
METHODS
new
Title : new
Usage : block_object = new Bio::NEXUS::TreesBlock($block_type, $commands, $verbose );
Function: Creates a new Bio::NEXUS::TreesBlock object and automatically reads the file
Returns : Bio::NEXUS::TreesBlock object
Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1; optional)
clone
Title : clone
Usage : my $newblock = $block->clone();
Function: clone a block object (shallow)
Returns : Block object
Args : none
set_trees
Title : set_trees
Usage : $block->set_trees($trees);
Function: Sets the list of trees (Bio::NEXUS::Tree objects)
Returns : none
Args : ref to array of Bio::NEXUS::Tree objects
add_tree
Title : add_tree
Usage : $block->add_tree($tree);
Function: Add trees (Bio::NEXUS::Tree object)
Returns : none
Args : a Bio::NEXUS::Tree object
add_tree_from_newick
Title : add_tree_from_newick
Usage : $block->add_tree_from_newick($newick_tree, $tree_name);
Function: Add a tree (Bio::NEXUS::Tree object)
Returns : none
Args : a tree string in newick format and a name for the tree (scalars)
get_trees
Title : get_trees
Usage : $block->get_trees();
Function: Gets the list of trees (Bio::NEXUS::Tree objects) and returns it
Returns : ref to array of Bio::NEXUS::Tree objects
Args : none
get_tree
Title : get_tree
Usage : $block->get_tree($treename);
Function: Gets the first tree (Bio::NEXUS::Tree object) that matches the name given or the first tree if $treename is not specified. If no tree matches, returns undef.
Returns : a Bio::NEXUS::Tree object
Args : tree name or none
set_translate
Title : set_translate
Usage : $block->set_translate($translate);
Function: Sets the hash of translates for nodes names
Returns : none
Args : hash of translates
translate
Title : translate
Usage : $self->translate($num);
Function: Translates a number with its associated name.
Returns : integer or string
Args : integer
Method : Returns the name associated with that numbers translated name.
If it cant find an association, returns the number.
reroot_tree
Title : reroot_tree
Usage : $block->reroot_tree($outgroup,$root_position, $treename);
Function: Reroot a tree using an OTU as new outgroup.
Returns : none
Args : outgroup name, the distance before the root position and tree name
reroot_all_trees
Title : reroot_all_trees
Usage : $block->reroot_all_trees($outgroup, $root_position);
Function: Reroot all the trees in the treesblock tree. use an OTU as new outgroup
Returns : none
Args : outgroup name and root position
rename_otus
Title : rename_otus
Usage : $block->rename_otus(%translation);
Function: Renames nodes based on a translation hash
Returns : none
Args : hash containing translation (e.g., { old_name => new_name} )
Comments: nodes not included in translation hash are unaffected
select_otus
Name : select_otus
Usage : $nexus->select_otus(@otunames);
Function: select a subset of OTUs
Returns : a new nexus object
Args : a ref to array of OTU names
select_tree
Name : select_tree
Usage : $nexus->select_tree($treename);
Function: select a tree
Returns : a new nexus object
Args : a tree name
select_subtree
Name : select_subtree
Usage : $nexus->select_subtree($inodename);
Function: select a subtree
Returns : a new nexus object
Args : an internal node name for subtree to be selected
exclude_subtree
Name : exclude_subtree
Usage : $nexus->exclude_subtree($inodename);
Function: remove a subtree
Returns : a new nexus object
Args : an internal node for subtree to be removed
equals
Name : equals
Usage : $nexus->equals($another);
Function: compare if two NEXUS objects are equal
Returns : boolean
Args : a NEXUS object
Download (0.15MB)
Added: 2006-12-19 License: Perl Artistic License Price:
1039 downloads
Bio::Factory::SequenceFactoryI 1.4
Bio::Factory::SequenceFactoryI is a Perl interface that allows for generic building of sequences in factories. more>>
Bio::Factory::SequenceFactoryI is a Perl interface that allows for generic building of sequences in factories which create sequences (like SeqIO).
SYNOPSIS
# do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like
use Bio::Seq::SeqFactory;
my $seqbuilder = new Bio::Seq::SeqFactory(type => Bio::PrimarySeq);
my $seq = $seqbuilder->create(-seq => ACTGAT,
-display_id => exampleseq);
print "seq is a ", ref($seq), "n";
A generic way to build Sequence objects via a pluggable factory. This reduces the amount of code that looks like
if( $type eq Bio::PrimarySeq ) { ... }
elsif( $type eq Bio::Seq::RichSeq ) { ... }
<<lessSYNOPSIS
# do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like
use Bio::Seq::SeqFactory;
my $seqbuilder = new Bio::Seq::SeqFactory(type => Bio::PrimarySeq);
my $seq = $seqbuilder->create(-seq => ACTGAT,
-display_id => exampleseq);
print "seq is a ", ref($seq), "n";
A generic way to build Sequence objects via a pluggable factory. This reduces the amount of code that looks like
if( $type eq Bio::PrimarySeq ) { ... }
elsif( $type eq Bio::Seq::RichSeq ) { ... }
Download (4.7MB)
Added: 2006-09-02 License: Perl Artistic License Price:
1147 downloads
Bio::AlignIO::msf 1.4
Bio::AlignIO::msf is a Perl module with msf sequence input/output stream. more>>
Bio::AlignIO::msf is a Perl module with msf sequence input/output stream.
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
This object can transform Bio::Align::AlignI objects to and from msf flat file databases.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream. Tries to read *all* MSF
It reads all non whitespace characters in the alignment
area. For MSFs with weird gaps (eg ~~~) map them by using
$al->map_chars(~,-)
Returns : L< Bio::Align::AlignI > object
Args : NONE
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in MSF format
Sequence type of the alignment is determined by the first sequence.
Returns : 1 for success and 0 for error
Args : L< Bio::Align::AlignI > object
<<lessSYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
This object can transform Bio::Align::AlignI objects to and from msf flat file databases.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream. Tries to read *all* MSF
It reads all non whitespace characters in the alignment
area. For MSFs with weird gaps (eg ~~~) map them by using
$al->map_chars(~,-)
Returns : L< Bio::Align::AlignI > object
Args : NONE
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in MSF format
Sequence type of the alignment is determined by the first sequence.
Returns : 1 for success and 0 for error
Args : L< Bio::Align::AlignI > object
Download (4.7MB)
Added: 2006-09-29 License: Perl Artistic License Price:
1121 downloads
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