Bio::SeqIO::gcg(3pm)

💖 Bio::SeqIO::gcg 💖

okay bestie, gather round, because this is the manual page for Bio::SeqIO::gcg — the GCG sequence input/output stream, straight outta the User Contributed Perl Documentation. yes it's a 3pm page, yes it's iconic, let's go ✨

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🌸 NAME 🌸

Bio::SeqIO::gcg — GCG sequence input/output stream. that's it, that's the name, slay 💅

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🦋 SYNOPSIS 🦋

Do not use this module directly.  Use it via the Bio::SeqIO class.

bestie do NOT come for this module directly, i'm begging 😭 go through Bio::SeqIO like a civilized person. it said what it said.

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✨ DESCRIPTION ✨

so this object? it can transform Bio::Seq objects to and from GCG flat file databases. back and forth, both directions, main character energy fr fr 👑

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💌 FEEDBACK 💌

🎀 Mailing Lists 🎀

user feedback is, like, integral to 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, no cap 🫶

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

🩷 Support 🩷

pls 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 who will be able to look at your problem and quickly address it. and if it's at all possible, include a thorough description of the problem with code and data examples — thoroughness is the vibe check, periodt 🌈

🐛 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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👑 AUTHORS - Ewan Birney & Lincoln Stein 👑

Email: <birney@ebi.ac.uk> <lstein@cshl.org>

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💜 CONTRIBUTORS 💜

Jason Stajich, jason@bioperl.org

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, the underscore means it's giving private 🔒)

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⭐ next_seq ⭐

• Title — next_seq
• Usage — $seq = $stream->next_seq()
• Function — returns the next sequence in the stream
• Returns — Bio::Seq object
• Args — (nothing, it's a no-args girly)

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🌟 write_seq 🌟

• Title — write_seq
• Usage — $stream->write_seq(@seq)
• Function — writes the formatted $seq object into the stream
• Returns — 1 for success and 0 for error
• Args — array of Bio::PrimarySeqI object

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🔥 GCG_checksum 🔥

• Title — GCG_checksum
• Usage — $cksum = $gcgio->GCG_checksum($seq);
• Function — returns a gcg checksum for the sequence specified

this method can also be called as a class method. versatile queen 💅

• Example — (blank, we love a mysterious icon)
• Returns — a GCG checksum string
• Argument — a Bio::PrimarySeqI implementing object

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🙈 _validate_checksum 🙈

• Title — _validate_checksum
• Usage — n/a - internal method
• Function — if parsed gcg sequence contains a checksum field
  • we compare it to a value computed here on the parsed
  • sequence. A checksum mismatch would indicate some
  • type of parsing failure occurred.
• Returns — 1 for success, 0 for failure
• Args — string containing parsed seq, value of parsed checksum

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and that's the whole page bestie, we ate and left absolutely no crumbs 🍓💅

perl v5.32.1 · 2021-08-15 — yeah this beauty is stamped from back in the day, Bio::SeqIO::gcg(3pm), and it's still serving. bye pookie, go parse some GCG files responsibly 🧚💖