Bio::S...nscript(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 NAME 💖

Bio::SeqFeature::Gene::Transcript — it's a feature that represents a transcript, bestie, that's the whole vibe ✨

✨ SYNOPSIS ✨

# See documentation of methods.

That's it. That's the whole synopsis. The actual deets live in the method docs, so go read those, okay? 💅

🦋 DESCRIPTION 🦋

Okay so lowkey: it's a feature representing a transcript. That's the entire description. Sometimes a class is just exactly what it says on the tin and we respect that fr fr 🎀

💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is integral to the evolution of this module and every other Bioperl module, no cap. Send your comments and suggestions to one of the Bioperl mailing lists — your participation is so appreciated, like genuinely 🫶

🫶 Support

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

bioperl-l@bioperl.org

...rather than sliding into the module maintainer's DMs directly 🙈 There are so many experienced and responsive experts on that list who will look at your problem and address it fast. If at all possible, include a thorough description of the problem along with code and data examples. The more context you give, the quicker someone can fix your thing. periodt 💯

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution together, as a team 🤝 Bug reports can be submitted via the web:

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

👑 AUTHOR - Hilmar Lapp 👑

Email: hlapp@gmx.net 🌸

part 2 incoming, bestie — don't go anywhere 💫

✨ APPENDIX ✨

okay bestie, this is the deep-lore section 💅 — the rest of the documentation, method by method. Internal methods are usually prefixed with an underscore _ (iykyk, that's just the secret handshake).

💖 promoters()

Title: promoters()

Usage:

@proms = $transcript->promoters();

Function: Get the promoter features/sites of this transcript.

⚠️ bestie I have to say this every time: OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. no cap.

Returns: An array of Bio::SeqFeatureI implementing objects representing the promoter regions or sites.

Args: (nothing, it just vibes)

💖 add_promoter()

Title: add_promoter()

Usage:

$transcript->add_promoter($feature);

Function: Add a promoter feature/site to this transcript.

⚠️ same warning, same energy: OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it.

Returns: (nothing)

Args: A Bio::SeqFeatureI implementing object.

💖 flush_promoters()

Title: flush_promoters()

Usage:

$transcript->flush_promoters();

Function: Remove all promoter features/sites from this transcript.

⚠️ yep, still: OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it.

Returns: the removed features as a list

Args: none

💖 exons()

Title: exons()

Usage:

@exons = $gene->exons();
($inital_exon) = $gene->exons('Initial');

Function: Get all exon features or all exons of specified type of this transcript.

Exon type is treated as a case-insensitive regular expression and is optional. For consistency, use only the following types: initial, internal, terminal.

Returns: An array of Bio::SeqFeature::Gene::ExonI implementing objects.

Args: An optional string specifying the primary_tag of the feature.

💖 exons_ordered()

Title: exons_ordered

Usage:

@exons = $gene->exons_ordered();
@exons = $gene->exons_ordered("Internal");

Function: Get an ordered list of all exon features or all exons of specified type of this transcript.

Exon type is treated as a case-insensitive regular expression and is optional. For consistency, use only the following types:

Returns: An array of Bio::SeqFeature::Gene::ExonI implementing objects.

Args: An optional string specifying the primary_tag of the feature.

💖 add_exon()

Title: add_exon()

Usage:

$transcript->add_exon($exon,'initial');

Function: Add a exon feature to this transcript.

The second argument denotes the type of exon. Mixing exons with and without a type is likely to cause trouble in exons(). Either leave out the type for all exons or for none.

Presently, the following types are known: initial, internal, terminal, utr, utr5prime, and utr3prime (all case-insensitive). UTR should better be added through utrs()/add_utr().

If you wish to use other or additional types, you will almost certainly have to call exon_type_sortorder() in order to replace the default sort order, or mrna(), cds(), protein(), and exons() may yield unexpected results. 😭

Returns: (nothing)

Args:

  • A Bio::SeqFeature::Gene::ExonI implementing object.
  • A string indicating the type of the exon (optional).

💖 flush_exons()

Title: flush_exons()

Usage:

$transcript->flush_exons();
$transcript->flush_exons('terminal');

Function: Remove all or a certain type of exon features from this transcript.

See add_exon() for documentation about types.

🚨 heads up bestie: calling without a type will not flush UTRs. Call flush_utrs() for this purpose.

Returns: the deleted features as a list

Args: A string indicating the type of the exon (optional).

💖 introns()

Title: introns()

Usage:

@introns = $gene->introns();

Function: Get all intron features this gene structure.

Note that this implementation generates these features on-the-fly, that is, it simply treats all regions between exons as introns, assuming that exons do not overlap. A consequence is that a consistent correspondence between the elements in the returned array and the array that exons() returns will exist only if the exons are properly sorted within their types (forward for plus-strand and reverse for minus-strand transcripts). To ensure correctness the elements in the array returned will always be sorted. ✨

Returns: An array of Bio::SeqFeature::Gene::Intron objects representing the intron regions.

Args: (nothing)

💖 poly_A_site()

Title: poly_A_site()

Usage:

$polyAsite = $transcript->poly_A_site();

Function: Get/set the poly-adenylation feature/site of this transcript.

Returns: A Bio::SeqFeatureI implementing object representing the poly-adenylation region.

Args: A Bio::SeqFeatureI implementing object on set, or FALSE to flush a previously set object.

💖 utrs()

Title: utrs()

Usage:

@utr_sites = $transcript->utrs('utr3prime');
@utr_sites = $transcript->utrs('utr5prime');
@utr_sites = $transcript->utrs();

Function: Get the features representing untranslated regions (UTR) of this transcript.

You may provide an argument specifying the type of UTR. Currently the following types are recognized: utr5prime utr3prime for UTR on the 5' and 3' end of the CDS, respectively.

Returns: An array of Bio::SeqFeature::Gene::UTR objects representing the UTR regions or sites.

Args: Optionally, either utr3prime, or utr5prime for the the type of UTR feature.

💖 add_utr()

Title: add_utr()

Usage:

$transcript->add_utr($utrobj, 'utr3prime');
$transcript->add_utr($utrobj);

Function: Add a UTR feature/site to this transcript.

The second parameter is optional and denotes the type of the UTR feature. Presently recognized types include 'utr5prime' and 'utr3prime' for UTR on the 5' and 3' end of a gene, respectively.

Calling this method is the same as calling add_exon($utrobj, 'utr'.$type). In this sense a UTR object is a special exon object, which is transcribed, not spliced out, but not translated. 🧬

🚨 note that the object supplied should return FALSE for is_coding(). Otherwise cds() and friends will become confused. don't do that to them.

Returns: (nothing)

Args: A Bio::SeqFeature::Gene::UTR implementing object.

💖 flush_utrs()

Title: flush_utrs()

Usage:

$transcript->flush_utrs();
$transcript->flush_utrs('utr3prime');

Function: Remove all or a specific type of UTR features/sites from this transcript.

Cf. add_utr() for documentation about recognized types.

Returns: a list of the removed features

Args: Optionally a string denoting the type of UTR feature.

💖 sub_SeqFeature()

Title: sub_SeqFeature

Usage:

@feats = $transcript->sub_SeqFeature();

Function: Returns an array of all subfeatures.

This method is defined in Bio::SeqFeatureI. We override this here to include the exon etc features.

Returns: An array Bio::SeqFeatureI implementing objects.

Args: none

💖 flush_sub_SeqFeature()

Title: flush_sub_SeqFeature

Usage:

$transcript->flush_sub_SeqFeature();
$transcript->flush_sub_SeqFeature(1);

Function: Removes all subfeatures.

This method is overridden from Bio::SeqFeature::Generic to flush all additional subfeatures like exons, promoters, etc., which is almost certainly not what you want. To remove only features added through $transcript->add_sub_SeqFeature($feature) pass any argument evaluating to TRUE.

Example: (none given)

Returns: none

Args: Optionally, an argument evaluating to TRUE will suppress flushing of all transcript-specific subfeatures (exons etc.).

💖 cds()

Title: cds

Usage:

$seq = $transcript->cds();

Function: Returns the CDS (coding sequence) as defined by the exons of this transcript and the attached sequence.

If no sequence is attached this method will return false.

Note that the implementation provided here returns a concatenation of all coding exons, thereby assuming that exons do not overlap.

Note also that you cannot set the CDS via this method. Set a single CDS feature as a single exon, or derive your own class if you want to store a predicted CDS.

Example: (none given)

Returns: A Bio::PrimarySeqI implementing object.

Args: (nothing)

💖 protein()

Title: protein()

Usage:

$protein = $transcript->protein();

Function: Get the protein encoded by the transcript as a sequence object.

The implementation provided here simply calls translate() on the object returned by cds().

Returns: A Bio::PrimarySeqI implementing object.

Args: (nothing)

💖 mrna()

Title: mrna()

Usage:

$mrna = $transcript->mrna();

Function: Get the mRNA of the transcript as a sequence object.

The difference to cds() is that the sequence object returned by this methods will also include UTR and the poly-adenylation site, but not promoter sequence (TBD).

HL: do we really need this method? 🤔

Returns: A Bio::PrimarySeqI implementing object.

Args: (nothing)

💖 features()

Title: features

Usage:

my @features=$transcript->features;

Function: returns all the features associated with this transcript

Returns: a list of SeqFeatureI implementing objects

Args: none

💖 features_ordered()

Title: features_ordered

Usage:

my @features=$transcript->features_ordered;

Function: returns all the features associated with this transcript, in order by feature start, according to strand ✨

Returns: a list of SeqFeatureI implementing objects

Args: none

and that's the whole page bestie, we made it to the end 🎀🦋 this one's from perl v5.32.1, dated 2021-08-15, and it's the man page for Bio::S...nscript(3pm) — go forth and annotate your transcripts, you absolute icon 👑💜

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