Bio::C...UniGene(3pm)

📦
version 1.7.3 · 2 versions
  • 1.7.3 · debian bookworm, debian trixie, ubuntu noble, ubuntu resolute, ubuntu stonking (latest)
  • 1.7.3 · ubuntu jammy
, in debian bookworm, debian trixie, ubuntu noble, ubuntu resolute, ubuntu stonking

🎀 NAME 🎀

okay bestie, welcome to the manual page for Bio::C...UniGene(3pm) — aka Bio::Cluster::UniGene — aka the UniGene object, and she is that girl 💅

✨ SYNOPSIS ✨

use Bio::Cluster::UniGene;
use Bio::ClusterIO;

$stream  = Bio::ClusterIO->new('-file' => "Hs.data",
                               '-format' => "unigene");
# note: we quote -format to keep older perl's from complaining.

while ( my $in = $stream->next_cluster() ) {
        print $in->unigene_id() . "\n";
        while ( my $sequence = $in->next_seq() ) {
                print $sequence->accession_number() . "\n";
        }
       }
⚠️ note the comment up there: quote -format, because older perls will literally complain otherwise. protect your peace (and your -format). 🫶

💖 DESCRIPTION 💖

So this UniGene object implements the Bio::Cluster::UniGeneI interface, and her whole job is representing UniGene clusters in Bioperl. She's the one the Bio::ClusterIO parser for unigene format hands back to you, and she holds all the data associated with one single UniGene record. one record, one object, no crumbs 🌸

She implements several interfaces, so you can drop her in anywhere an instance of those interfaces is expected. Specifically: Bio::ClusterI as the base interface for all cluster representations, plus Bio::IdentifiableI and Bio::DescribableI. iconic behaviour, honestly 👑

Here's the full rundown of the UniGene-specific methods available (details further down). 🚨 real talk though: the next_XXX iterators take a snapshot of the array property the first time you call them, and that snapshot does not get reset until the iterator is exhausted. So like… once you've called it, you have to fully exhaust the iterator before you'll see any changes made to the property in the meantime. no cap. You will usually want to use the non-iterator equivalents and loop over the elements yourself. 💀

  • new() - standard new call
  • unigene_id() - set/get unigene_id
  • title() - set/get title (description)
  • gene() - set/get gene
  • cytoband() - set/get cytoband
  • mgi() - set/get mgi
  • locuslink() - set/get locuslink
  • homol() - set/get homologene
  • gnm_terminus() - set/get gnm_terminus
  • scount() - set/get scount
  • express() - set/get express, currently takes/returns a reference to an array of expressed tissues
  • next_express() - returns the next tissue expression from the expressed tissue array
  • chromosome() - set/get chromosome, currently takes/returns a reference to an array of chromosome lines
  • next_chromosome() - returns the next chromosome line from the array of chromosome lines
  • sts() - set/get sts, currently takes/returns a reference to an array of sts lines
  • next_sts() - returns the next sts line from the array of sts lines
  • txmap() - set/get txmap, currently takes/returns a reference to an array of txmap lines
  • next_txmap() - returns the next txmap line from the array of txmap lines
  • protsim() - set/get protsim, currently takes/returns a reference to an array of protsim lines
  • next_protsim() - returns the next protsim line from the array of protsim lines
  • sequences() - set/get sequence, currently takes/returns a reference to an array of references to seq info
  • next_seq() - returns a Seq object that currently only contains an accession number

🦋 Implemented Interfaces 🦋

She's out here implementing the following interfaces, and yes she serves in all of them:

  • Bio::Cluster::UniGeneI — this includes implementing Bio::ClusterI.
  • Bio::IdentifiableI
  • Bio::DescribableI
  • Bio::AnnotatableI
  • Bio::Factory::SequenceStreamI

🌸 FEEDBACK 🌸

💌 Mailing Lists 💌

User feedback is an integral part of the evolution of this and other Bioperl modules. so like, send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated, fr fr 🫶

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫶 Support 🫶

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and responsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. the more deets the better, bestie 💅

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

👑 AUTHOR - Andrew Macgregor 👑

Email andrew at cbbc.murdoch.edu.au

🌈 CONTRIBUTORS 🌈

Hilmar Lapp, hlapp at gmx.net

📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. 🧚

✨ new ✨

  • Title : new
  • Usage : used by ClusterIO
  • Returns : a new Bio::Cluster::Unigene object

💅 Bio::Cluster::UniGeneI methods 💅

🌸 unigene_id 🌸

  • Title : unigene_id
  • Usage : unigene_id();
  • Function: Returns the unigene_id associated with the object.
  • Example : $id = $unigene->unigene_id or $unigene->unigene_id($id)
  • Returns : A string
  • Args : None or an id

🎀 title 🎀

  • Title : title
  • Usage : title();
  • Function: Returns the title associated with the object.
  • Example : $title = $unigene->title or $unigene->title($title)
  • Returns : A string
  • Args : None or a title

🌷 gene 🌷

  • Title : gene
  • Usage : gene();
  • Function: Returns the gene associated with the object.
  • Example : $gene = $unigene->gene or $unigene->gene($gene)
  • Returns : A string
  • Args : None or a gene

🦋 cytoband 🦋

  • Title : cytoband
  • Usage : cytoband();
  • Function: Returns the cytoband associated with the object.
  • Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband)
  • Returns : A string
  • Args : None or a cytoband

💜 mgi 💜

  • Title : mgi
  • Usage : mgi();
  • Function: Returns the mgi associated with the object.
  • Example : $mgi = $unigene->mgi or $unigene->mgi($mgi)
  • Returns : A string
  • Args : None or a mgi
  • Title : locuslink
  • Usage : locuslink();
  • Function: Returns or stores a reference to an array containing locuslink data.
  • Returns : An array reference
  • Args : None or an array reference

⭐ homol ⭐

  • Title : homol
  • Usage : homol();
  • Function: Returns the homol entry associated with the object.
  • Example : $homol = $unigene->homol or $unigene->homol($homol)
  • Returns : A string
  • Args : None or a homol entry

🌈 restr_expr 🌈

  • Title : restr_expr
  • Usage : restr_expr();
  • Function: Returns the restr_expr entry associated with the object.
  • Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr)
  • Returns : A string
  • Args : None or a restr_expr entry

🧚 gnm_terminus 🧚

  • Title : gnm_terminus
  • Usage : gnm_terminus();
  • Function: Returns the gnm_terminus associated with the object.
  • Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus)
  • Returns : A string
  • Args : None or a gnm_terminus

💫 scount 💫

  • Title : scount
  • Usage : scount();
  • Function: Returns the scount associated with the object.
  • Example : $scount = $unigene->scount or $unigene->scount($scount)
  • Returns : A string
  • Args : None or a scount

🔥 express 🔥

  • Title : express
  • Usage : express();
  • Function: Returns or stores a reference to an array containing tissue expression data
  • Returns : An array reference
  • Args : None or an array reference

🧬 chromosome 🧬

  • Title : chromosome
  • Usage : chromosome();
  • Function: Returns or stores a reference to an array containing chromosome lines
  • Returns : An array reference
  • Args : None or an array reference

💖 sts 💖

  • Title : sts
  • Usage : sts();
  • Function: Returns or stores a reference to an array containing sts lines
  • Returns : An array reference
  • Args : None or an array reference

🌟 txmap 🌟

  • Title : txmap
  • Usage : txmap();
  • Function: Returns or stores a reference to an array containing txmap lines
  • Returns : An array reference
  • Args : None or an array reference

👑 protsim 👑

  • Title : protsim
  • Usage : protsim();
  • Function: Returns or stores a reference to an array containing protsim lines This should really only be used by ClusterIO, not directly
  • Returns : An array reference
  • Args : None or an array reference

🐚 sequences 🐚

  • Title : sequences
  • Usage : sequences();
  • Function: Returns or stores a reference to an array containing sequence data.

This is mostly reserved for ClusterIO parsers. You should use get_members() for get and add_member()/remove_members() for set.

  • Returns : An array reference, or undef
  • Args : None or an array reference or undef

🌸 species 🌸

  • Title : species
  • Usage : $obj->species($newval)
  • Function: Get/set the species object for this Unigene cluster.
  • Example :
  • Returns : value of species (a L<Bio::Species> object)
  • Args : on set, new value (a L<Bio::Species> object or the binomial name, or undef, optional)

💜 Bio::ClusterI methods 💜

✨ display_id ✨

  • Title : display_id
  • Usage :
  • Function: Get/set the display name or identifier for the cluster

This is aliased to unigene_id().

  • Returns : a string
  • Args : optional, on set the display ID ( a string)

🎀 description 🎀

  • Title : description
  • Usage : Bio::ClusterI->description("POLYUBIQUITIN")
  • Function: get/set for the consensus description of the cluster

This is aliased to title().

  • Returns : the description string
  • Args : Optional the description string

🌷 size 🌷

  • Title : size
  • Usage : Bio::ClusterI->size();
  • Function: get for the size of the family, calculated from the number of members

This is aliased to scount().

  • Returns : the size of the cluster
  • Args :

🦋 cluster_score 🦋

  • Title : cluster_score
  • Usage : $cluster ->cluster_score(100);
  • Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster.

For UniGene clusters, there really is no cluster score that would come with the data. However, we provide an implementation here so that you can score UniGene clusters if you want to.

  • Returns : a number
  • Args : optionally, on set a number

💅 get_members 💅

  • Title : get_members
  • Usage : Bio::ClusterI->get_members(($seq1, $seq2));
  • Function: retrieve the members of the family by some criteria

Will return all members if no criteria are provided.

At this time this implementation does not support specifying criteria and will always return all members.

  • Returns : the array of members
  • Args :

🫶 Annotatable view at the object properties

annotation

  • Title: annotation
  • Usage: $obj->annotation($newval)
  • Function: Get/set the Bio::AnnotationCollectionI object for this UniGene cluster.

Okay so bestie, listen — a whole bunch of this class's attributes are actually stashed inside the annotation collection object as Bio::AnnotationI compliant objects. Which is iconic, actually, because it means you can poke at them through the same interface you'd use to reach, like, Bio::SeqI annotation properties. So convenient, no cap.

⚠️ But real talk: if you call this method in set mode and swap the annotation collection out for a different one, you should know exactly what you're doing. That's a big-girl move, not a casual one. 💀
  • Example: (none given)
  • Returns: a Bio::AnnotationCollectionI compliant object
  • Args: on set, new value (a Bio::AnnotationCollectionI compliant object or undef, optional)

💅 Implementation specific methods

These are mostly for adding/removing to array properties, and for methods with special functionality. iykyk.

add_member

  • Title: add_member
  • Usage: (none given)
  • Function: Adds a member object to the list of members.
  • Example: (none given)
  • Returns: TRUE if the new member was successfully added, and FALSE otherwise.
  • Args: The member to add.

remove_members

  • Title: remove_members
  • Usage: (none given)
  • Function: Remove the list of members for this cluster such that the member list is undefined afterwards (as opposed to zero members — different vibe entirely, bestie).
  • Example: (none given)
  • Returns: the previous list of members
  • Args: none
  • Title: next_locuslink
  • Usage: next_locuslink();
  • Function: Returns the next locuslink from an array referred to using $obj->{'locuslink'}

If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. 🌀

  • Example:
     while ( my $locuslink = $in->next_locuslink() ) {
                                    print "$locuslink\n";
                            }
  • Returns: String
  • Args: None

next_express

  • Title: next_express
  • Usage: next_express();
  • Function: Returns the next tissue from an array referred to using $obj->{'express'}

If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator.

  • Example:
     while ( my $express = $in->next_express() ) {
                                    print "$express\n";
                            }
  • Returns: String
  • Args: None

next_chromosome

  • Title: next_chromosome
  • Usage: next_chromosome();
  • Function: Returns the next chromosome line from an array referred to using $obj->{'chromosome'}

If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator.

  • Example:
     while ( my $chromosome = $in->next_chromosome() ) {
                                    print "$chromosome\n";
                            }
  • Returns: String
  • Args: None

next_protsim

  • Title: next_protsim
  • Usage: next_protsim();
  • Function: Returns the next protsim line from an array referred to using $obj->{'protsim'}

If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator.

  • Example:
     while ( my $protsim = $in->next_protsim() ) {
                                    print "$protsim\n";
                            }
  • Returns: String
  • Args: None

next_sts

  • Title: next_sts
  • Usage: next_sts();
  • Function: Returns the next sts line from an array referred to using $obj->{'sts'}

If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator.

  • Example:
     while ( my $sts = $in->next_sts() ) {
                                    print "$sts\n";
                            }
  • Returns: String
  • Args: None

next_txmap

  • Title: next_txmap
  • Usage: next_txmap();
  • Function: Returns the next txmap line from an array referred to using $obj->{'txmap'}

If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator.

  • Example:
     while ( my $tsmap = $in->next_txmap() ) {
                                    print "$txmap\n";
                            }
  • Returns: String
  • Args: None

🌈 Bio::IdentifiableI methods

object_id

  • Title: object_id
  • Usage: $string = $obj->object_id()
  • Function: a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences.

This is aliased to unigene_id().

  • Returns: A scalar

version

  • Title: version
  • Usage: $version = $obj->version()
  • Function: a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept.

Unigene clusters usually won't have a version, so this will be mostly undefined. 🙈

  • Returns: A number
  • Args: on set, new value (a scalar or undef, optional)

authority

  • Title: authority
  • Usage: $authority = $obj->authority()
  • Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org)
  • Returns: A scalar
  • Args: on set, new value (a scalar or undef, optional)

namespace

  • Title: namespace
  • Usage: $string = $obj->namespace()
  • Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection
  • Returns: A scalar
  • Args: on set, new value (a scalar or undef, optional)

🎀 Bio::DescribableI methods

display_name

  • Title: display_name
  • Usage: $string = $obj->display_name()
  • Function: A string which is what should be displayed to the user. The string should have no spaces (ideally — though a cautious user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea, bestie, trust).

This is aliased to unigene_id().

  • Returns: A scalar
  • Status: Virtual

description()

  • Title: description
  • Usage: $string = $obj->description()
  • Function: A text string suitable for displaying to the user a description. This string is likely to have spaces, but should not have any newlines or formatting — just plain text. The string should not be greater than 255 characters and clients can feel justified at truncating strings at 255 characters for the purposes of display.

This is already demanded by Bio::ClusterI and hence is present anyway. 💁

  • Returns: A scalar

🦋 Bio::Factory::SequenceStreamI methods

next_seq

  • Title: next_seq
  • Usage: next_seq();
  • Function: Returns the next seq as a Seq object as defined by $seq->sequence_factory(), at present an empty Bio::Seq::RichSeq object with just the accession_number() and pid() set.

This iterator will not exhaust the array of member sequences. If you call next_seq() again after it returned undef, it will re-cycle through the list of member sequences. 🔁

  • Example:
  while ( my $sequence = $in->next_seq() ) {
    print $sequence->accession_number() . "\n";
   }
  • Returns: Bio::PrimarySeqI object
  • Args: None

sequence_factory

  • Title: sequence_factory
  • Usage: $seqio->sequence_factory($seqfactory)
  • Function: Get/Set the Bio::Factory::SequenceFactoryI
  • Returns: Bio::Factory::SequenceFactoryI
  • Args: [optional] Bio::Factory::SequenceFactoryI

🔒 Private methods

These are private, bestie. Hands off unless you wrote them. 🤫

_annotation_value

  • Title: _annotation_value
  • Usage: (none given)
  • Function: Private method.
  • Example: (none given)
  • Returns: the value (a string)
  • Args: annotation key (a string); on set, annotation value (a string)

_annotation_value_ary

  • Title: _annotation_value_ary
  • Usage: (none given)
  • Function: Private method.
  • Example: (none given)
  • Returns: reference to the array of values
  • Args: annotation key (a string); on set, reference to an array holding the values
  • Title: _annotation_dblink
  • Usage: (none given)
  • Function: Private method.
  • Example: (none given)
  • Returns: array of accessions for the given database (namespace)
  • Args: annotation key (a string); dbname (a string) (optional on get, mandatory on set); on set, accession or ID (a string), and version
  • Title: _remove_dblink
  • Usage: (none given)
  • Function: Private method.
  • Example: (none given)
  • Returns: array of accessions for the given database (namespace)
  • Args: annotation key (a string); dbname (a string) (optional)

And that's a wrap on the whole page, bestie. 🫶✨ This one came from the Perl docs built with perl v5.34.0 and stamped 2022-03-27 — so if you're reading this years later, just know the vibes are vintage but the API is forever. Go cluster some genes, you absolute icon. 💖🧬👑

📦 where this page comes from