Bio::F...StreamI(3pm)

💖 Bio::F...StreamI(3pm) — the vibe ✨

okay bestie, so this page is from the User Contributed Perl Documentation, and it's literally called Bio::F...StreamI on the tin (the full name is Bio::Factory::SequenceStreamI, iykyk, the man page just truncates it like that 🫶).

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🌸 NAME 🌸

Bio::Factory::SequenceStreamI — it's an interface, and it describes the basics of a Sequence Stream. that's the whole job. it's giving "job description, not the job" energy 💅

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✨ SYNOPSIS ✨

you grab a SequenceStreamI object somehow, kinda like you'd do with SeqIO:

# get a SequenceStreamI object somehow like with SeqIO
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-file => '< fastafile');
while( my $seq = $in->next_seq ) {
}

that's it, that's the vibe check 🌈

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🦋 DESCRIPTION 🦋

so this interface is for describing objects that either produce Bio::PrimarySeqI objects, or process Bio::PrimarySeqI objects out to a data stream. basically: things that make seqs, things that eat seqs. iconic behavior either way 💖

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🎀 FEEDBACK 🎀

💌 Mailing Lists

user feedback is, like, an integral part of the evolution of this and other Bioperl modules, fr fr. send your comments and suggestions preferably to the Bioperl mailing list. 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

...and not to the module maintainer directly, bestie, i'm begging 🙈 there are so many experienced and reponsive experts who will be able to 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, because that's the difference between "slay, fixed" and "ma'am what" 😭

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of 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 - Jason Stajich 👑

email jason@bioperl.org

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🌟 APPENDIX 🌟

the rest of the documentation goes into detail on each of the object methods. internal methods are usually preceded with a _ (iykyk, that underscore is the "don't touch, that's my emotional support private method" marker 💀).

🍓 next_seq

• Title : next_seq
• Usage : $seq = stream->next_seq
• Function : reads the next sequence object from the stream and returns it.

okay so here's the tea: certain driver modules may encounter entries in the stream that are either misformatted or that use syntax not yet understood by the driver. if such an incident is recoverable — like, say, by dismissing a feature of a feature table or some other non-mandatory part of an entry — the driver will issue a warning. but in the case of a non-recoverable situation, an exception will be thrown. ⚠️ do not assume that you can resume parsing the same stream after catching the exception. note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2).

• Returns : a Bio::Seq sequence object
• Args : none

see Bio::Root::RootI 💜

🧚 write_seq

• Title : write_seq
• Usage : $stream->write_seq($seq)
• Function : writes the $seq object into the stream
• Returns : 1 for success and 0 for error
• Args : Bio::Seq object

💫 sequence_factory

• Title : sequence_factory
• Usage : $seqio->sequence_factory($seqfactory)
• Function : get the Bio::Factory::SequenceFactoryI
• Returns : Bio::Factory::SequenceFactoryI
• Args : none

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and that's a wrap, bestie! 🌈 this lil' slice of lore was brought to you by perl v5.32.1, dated 2021-08-15, filed under Bio::F...StreamI(3pm). go forth and stream those sequences responsibly, periodt 💅✨🎀