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

💖 NAME 💖

Bio::Matrix::PSM::InstanceSite — a PSM site occurrence. That's it, that's the whole vibe. ✨

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🌸 SYNOPSIS 🌸

okay bestie, here's how you actually get one of these:

use Bio::Matrix::PSM::InstanceSite;

#You 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, -anchor=>'CHR7', -start=>35000921, -end=>35000926);

#Last 2 arguments are passed to create a Bio::LocatableSeq object
#Anchor shows the coordinates system for the Bio::LocatableSeq object

like. either you pull it out of a file, or you build it in memory. both are valid. 💅

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🦋 DESCRIPTION 🦋

So InstanceSite is the abstract interface to a PSM site occurrence — and by "PSM" we mean a PSM sequence match, iykyk. You use InstanceSite objects to describe a PSM match (and if you wanna know about the matrix side of things, go look at Bio::Matrix::PSM::SiteMatrix).

The usual deets that come with one of these matches are: sequence coordinates, score, sequence, and a sequence (gene) identifier — which could be an accession number or literally any other id. all of it, in one little object. 🫶

This object inherits from Bio::LocatableSeq, and that's the thing that actually defines the real sequence. On top of that, it might also hold a SiteMatrix object — either the one used to detect the CRE (that's a cis-regulatory element, bestie) or one that got created from this CRE.

⚠️ now the tea: the docs say the motif id + gene id (accession) combo should be unique. This is not entirely true. There can be more than one occurrence of the same cis-regulatory element in the upstream region of the same gene. So to build a really unique combo, you need relpos as the third element. three-part key, no cap. 🔑

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🎀 FEEDBACK 🎀

💌 Mailing Lists

User feedback is literally an integral part of the evolution of this module and all the other Bioperl modules, so don't be shy — send your comments and suggestions to one of the Bioperl mailing lists. Your participation is much appreciated. genuinely. 🥹

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

🫂 Support

kay so for usage questions and support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

...instead of going straight to the module maintainer. there are so many experienced and responsive experts hanging out there who'll look at your problem and address it fast. and please, pretty please, include a thorough description of the problem with code and data examples if at all possible. the more context, the faster the fix. 💖

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions. Bug reports can be submitted via the web:

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

📝 Description

Bio::Matrix::PSM::InstanceSiteI implementation. that's the whole note. ✨

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👑 AUTHOR — Stefan Kirov 👑

Email: skirov@utk.edu

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🌈 APPENDIX 🌈

🧚 new

• Title — new
• Usage —

my $isntance=Bio::Matrix::PSM::InstanceSite->new
                        (-seq=>'TATAAT', -id=>"TATAbox1",
                         -accession_number='ENSG00000122304', -mid=>'TB1',
                         -desc=>'TATA box, experimentally verified in PRM1 gene',
                         -relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926, strand=>1)

• Function — Creates an InstanceSite object from memory. yes, from memory, no file needed. 🧠✨
• Throws — (nothing listed — left blank in the source)
• Example — (nothing listed — left blank in the source)
• Returns — Bio::Matrix::PSM::InstanceSite object
• Args — hash

🌟 mid

• Title — mid
• Usage — my $mid=$instance->mid;
• Function — Get/Set the motif id
• Throws — (nothing listed — left blank in the source)
• Example — (nothing listed — left blank in the source)
• 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 — (nothing listed — left blank in the source)
• Example — (nothing listed — left blank in the source)
• Returns — real number
• Args — real number

⚓ anchor

• Title — anchor
• Usage — my $anchor=$instance->anchor;
• Function — Get/Set the anchor, which shows what coordinate system start/end use
• Throws — (nothing listed — left blank in the source)
• Example — (nothing listed — left blank in the source)
• Returns — string
• Args — string

🎯 start

• Title — start
• Usage — my $start=$instance->start;
• Function — Get/Set the position of the instance on the sequence used
• Throws — (nothing listed — left blank in the source)
• Example — (nothing listed — left blank in the source)
• Returns — integer
• Args — integer

🪪 minstance

• Title — minstance
• Usage — my $minstance=$misntance->score;
• Function — Get/Set the unique identifier — sequence id / motif id, like PRM1_TATAbox for example. Not necessarily human readable, so don't come for it. 🙈
• Throws — (nothing listed — left blank in the source)
• Example — (nothing listed — left blank in the source)
• Returns — string
• Args — string

📍 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 be negative — and usually is. 📉
• Throws — (nothing listed — left blank in the source)
• Example — (nothing listed — left blank in the source)
• Returns — integer
• Args — integer

🏷️ annotation

• Title — annotation
• Usage — $ann = $seq->annotation or $seq->annotation($annotation)
• Function — Gets or sets the annotation
• Returns — Bio::AnnotationCollectionI object
• Args — None or Bio::AnnotationCollectionI object

See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information. 💜

🦠 species

• Title — species
• Usage — $species = $seq->species() or $seq->species($species)
• Function — Gets or sets the species
• Returns — Bio::Species object
• Args — None or Bio::Species object

See Bio::Species for more information. 💜

🖼️ frame

• Title — frame
• Usage — my $frane=$instance->frame;
• Function — Get/Set the frame of a DNA instance with respect to a protein motif used. Returns undef if the motif was not protein or the DB is protein.
• Throws — (nothing listed — left blank in the source)
• Example — (nothing listed — left blank in the source)
• Returns — integer
• Args — integer (0, 1, 2)

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🫶 and that's the whole page, bestie. every flag, every arg, every blank Throws field, all of it. no skips. periodt.

this absolute icon of a page is part of the User Contributed Perl Documentation, and it's sitting at perl v5.32.1, dated 2021-08-15. slay. 💅✨