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

💖 Bio::C...iGeneI(3pm) 💖

okay so this is the manual page for Bio::C...iGeneI(3pm), and it comes to you courtesy of the User Contributed Perl Documentation collection. it's a Perl module doc, it's an abstract interface, and honestly? she's serving. let's get into it bestie 🦋✨

---

🌸 NAME 🌸

Bio::Cluster::UniGeneI — abstract interface of UniGene object

---

✨ SYNOPSIS ✨

the entire synopsis is literally one character. it's a comment. that's the whole vibe:

#

---

🧚 DESCRIPTION 🧚

so this is the general interface for a UniGene cluster representation in Bioperl. and here's the thing — you cannot use this module directly, bestie. use an implementation instead. it's an interface, not a whole meal 💅

you can create UniGene cluster objects yourself by instantiating Bio::Cluster::UniGene. and if you read UniGene clusters from a ClusterIO parser, you'll get objects that implement this interface — most likely instances of that UniGene class we just mentioned.

also important: Bio::Cluster::UniGeneI inherits from Bio::ClusterI, so you can use it wherever a cluster object is expected. versatile queen 👑

---

💌 FEEDBACK 💌

#

📬 Mailing Lists

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

• 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 reponsive experts will be able look at the problem and quickly address it. (yes it says "reponsive" in the source, we keep it, no cap 💀) please include a thorough description of the problem with code and data examples if at all possible.

🐛 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

---

📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a "_". so if you see an underscore, that's a private lil thing, iykyk 🤫

---

🌟 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

🌟 locuslink

• Title: locuslink
• Usage: locuslink();
• Function: Returns or stores a reference to an array containing locuslink data. This should really only be used by ClusterIO, not directly.
• 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. This should really only be used by ClusterIO, not directly.
• 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. This should really only be used by ClusterIO, not directly.
• 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. This should really only be used by ClusterIO, not directly.
• 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

🌟 sequence

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

🌟 species

• Title: species
• Usage: $obj->species($newval)
• Function: Get the species object for this Unigene cluster.
• Example: (nothing here in the source, she's mysterious 🙈)
• Returns: value of species (a L<Bio::Species> object)
• Args: (also empty, no thoughts, head empty 🎀)

---

🦋 Methods inherited from Bio::ClusterI 🦋

💫 display_id

• Title: display_id
• Usage: (blank in the source)
• Function: Get/set the display name or identifier for the cluster
• 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
• Returns: the description string
• Args: Optional the description string

💫 size

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

💫 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.
• Returns: a number

💫 get_members

• Title: get_members
• Usage: Bio::ClusterI->get_members(($seq1, $seq2));
• Function: retrieve the members of the family by some criteria, for example: $cluster->get_members(-species => 'homo sapiens'); Will return all members if no criteria are provided.
• Returns: the array of members
• Args: (blank)

---

and that's the whole page bestie 🫶 every method documented, every default accounted for, nothing skipped. main character documentation energy only 💅✨

that's a wrap! this page is from perl v5.34.0, dated 2022-03-27, filed under Bio::C...iGeneI(3pm). go forth and cluster, queen 👑🌸💖