Bio::U...bleSeqI(3pm)

💖 NAME 💖

Bio::UpdateableSeqI — it's a descendant of Bio::SeqI that allows updates 💅

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✨ SYNOPSIS ✨

Bestie, most of the documentation lives over in Bio::SeqI, okay? And then the individual methods have their own docs with the deets. Go look at those 👑

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🦋 DESCRIPTION 🦋

So Bio::UpdateableSeqI is an interface for Sequence objects that are expected to let users do the basic editing stuff — think update/delete — on their component SeqFeatures. It's giving "let me edit my features" energy and honestly? We love that for it 💖

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🌸 FEEDBACK 🌸

🎀 Mailing Lists 🎀

User feedback is literally an integral part of the evolution of this and other Bioperl modules — like, the whole thing grows because y'all talk to us 🫶 So send your comments and suggestions preferably to the Bioperl mailing list. 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 sliding into the module maintainer's DMs directly, okay? 🙈 There are many experienced and responsive experts who will be able to look at the problem and quickly address it. And if it's at all possible, please include a thorough description of the problem with code and data examples. The more context, the better the vibe check 🔥

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — it's a whole thing, and we're obsessed with staying organised. Bug reports can be submitted via the web:

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

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👑 AUTHOR - David Block 👑

Email dblock@gene.pbi.nrc.ca

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🌈 CONTRIBUTORS 🌈

Ewan Birney forced me to this...

Not me getting peer-pressured into writing a manpage 😭 iconic behaviour honestly.

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📖 APPENDIX 📖

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

🍓 delete_feature 🍓

Title   : delete_feature
Usage   : my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
          or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent.  Keeps track of the features
          of the $gene object that may be left as orphans and returns them as a listref.
Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
          This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
          my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
          $orphanlist is a reference to a list containing $exon{'2'};
Returns : a listref of orphaned features after the deletion of $feature (optional)
Args    : $feature - the feature to be deleted
          $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
                        transcripts in a gene.
          $gene - the gene containing the $transcript and/or the $feature

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And that's the whole page, bestie!! This one's from Bio::U...bleSeqI(3pm) in the perl v5.32.1 docs, dated 2021-08-15 — yeah, it's a lil vintage but she still slays 💅✨