Bio::M...ceSiteI(3pm)

✨ Bio::Matrix::PSM::InstanceSiteI 💖

okay bestie, welcome to the Bio::Matrix::PSM::InstanceSiteI page from the User Contributed Perl Documentation 💅 this is the InstanceSite interface, and it holds an instance of a PSM. yes queen, one single instance. let's get into it 🦋

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🌸 NAME 🌸

Bio::Matrix::PSM::InstanceSiteI — it's the InstanceSite interface, and it holds an instance of a PSM. that's the whole vibe. 🎀

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✨ SYNOPSIS ✨

use Bio::Matrix::PSM::InstanceSite;
#Y ou can get an InstanceSite object either from a file:
my ($instances,$matrix)=$SomePSMFile->parse_next;
#or from memory
my %params=(seq       => 'TATAAT',
            id        => "TATAbox1",
            accession => 'ENSG00000122304',
            mid       => 'TB1',
            desc      => 'TATA box, experimentally verified in PRM1 gene',
            relpos    => -35);

so like, you can pull an InstanceSite object out of a file with parse_next, or you can just build one from memory with a %params hash. either way, slay. 🫶 (and yes, the #Y ou spacing is exactly how it's written in the source, no cap, we don't fix other people's comments 💀)

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👑 DESCRIPTION 👑

so this is the abstract interface to a PSM site occurrence (that's a PSM sequence match, iykyk).

InstanceSite objects can be used to describe a PSM sequence match — PSM here meaning Bio::Matrix::PSM::SiteMatrix, go look at that page too bestie.

the usual characteristic of such a match is:

• sequence coordinates
• score
• sequence
• sequence (gene) identifier — either an accession number or some other id

this object inherits from Bio::LocatableSeq, which is the thing that defines the real sequence. and it might also hold a SiteMatrix object, which is used to detect the CRE (that's a cis-regulatory element), or it was created from that CRE. either direction, we love that for it. 💜

okay so here's the tea 🍵 the docs say the motif id + gene id (accession) combo should be unique. that is not entirely true. there might be more than one occurrence of the same cis-regulatory element in the upstream region of the same gene. so relpos would be the third element you need to create a really unique combination. three-part key, iconic behaviour honestly.

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💌 FEEDBACK 💌

🌈 Mailing Lists 🌈

user feedback is an integral part of the evolution of this and other Bioperl modules. so 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 reponsive 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. give them the full picture bestie, they'll eat it up. ✨

🐛 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

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💫 AUTHOR - Stefan Kirov 💫

Email skirov@utk.edu

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🦋 SEE ALSO 🦋

• Bio::Matrix::PSM::SiteMatrix
• Bio::Matrix::PSM::Psm
• Bio::Matrix::PSM::IO

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📖 APPENDIX 📖

🎀 mid 🎀

• Title : mid
• Usage : my $mid=$instance->mid;
• Function: get/set the motif id
• Throws :
• Returns : scalar
• Args : scalar

🎀 score 🎀

• Title : score
• Usage : my $score=$instance->score;
• Function: get/set the score (mismatches) between the instance and the attached (or initial) PSM
• Throws :
• Returns : real number
• Args : real number

🎀 start 🎀

• Title : start
• Usage : my $start=$instance->start;
• Function: get/set the position of the instance on the sequence used
• Throws :
• Returns : integer
• Args : integer

🎀 relpos 🎀

• Title : relpos
• Usage : my $seqpos=$instance->relpos;
• Function: get/set the relative position of the instance with respect to the transcription start site (if known). can and usually is negative. yes, negative. it's giving upstream energy. 🙈
• Throws :
• Returns : integer
• Args : integer

🎀 minstance 🎀

• Title : minstance
• Usage : my $minstance=$misntance->score;
• Function: get/set the unique identifier — sequence id/motif id, for example PRM1_TATAbox. not necessarily human readable. (and no, that $misntance typo in the Usage line is the original, we are preserving it with love 💀)
• Throws :
• Returns : string
• Args : string

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and that's the whole page, bestie!! 🎉 this one came to you from perl v5.32.1, dated 2021-08-15, living its best life as Bio::M...ceSiteI(3pm). mwah, go build something iconic with it 💖✨🎀🦋