Bio::A...ustalw(3pm)

💖 Bio::AlignIO::clustalw — the whole vibe 💖

okay bestie, so this is the man page for Bio::AlignIO::clustalw, which lives in the User Contributed Perl Documentation and is documented as Bio::A...ustalw(3pm) because terminals love to truncate things for no reason. 🙈 It's clustalw sequence input/output stream energy, and we're gonna get into it.

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✨ NAME ✨

Bio::AlignIO::clustalw — clustalw sequence input/output stream. that's it, that's the name, slay. 💅

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🌸 SYNOPSIS 🌸

bestie do NOT come for this module directly. like, at all.

Do not use this module directly. Use it via the Bio::AlignIO class. that's the whole synopsis. short, iconic, non-negotiable. 👑

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🦋 DESCRIPTION 🦋

This object can transform Bio::Align::AlignI objects to and from clustalw files. so it's basically a little translator goblin that speaks both "Perl object" and "clustalw file" and it's fluent in both. 🧚

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like fr fr, your thoughts literally shape the future of these modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. 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 and support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. the way that many experienced and reponsive experts will be able look at the problem and quickly address it… like, there's a whole squad waiting to help you. 💖 Please include a thorough description of the problem with code and data examples if at all possible — the more deets the better, no gatekeeping your own bug.

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track 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 — Peter Schattner 👑

Email: schattner@alum.mit.edu

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — that underscore is the "do not perceive me" marker, iykyk. 🙈

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✨ new ✨

Title   : new
Usage   : $alignio = Bio::AlignIO->new(-format => 'clustalw',
                      -file => 'filename');
Function: returns a new Bio::AlignIO object to handle clustalw files
Returns : Bio::AlignIO::clustalw object
Args    : -verbose => verbosity setting (-1, 0, 1, 2)
          -file    => name of file to read in or to write, with ">"
          -fh      => alternative to -file param - provide a filehandle
                      to read from or write to
          -format  => alignment format to process or produce
          -percentages => display a percentage of identity
                          in each line of the alignment (clustalw only)
          -linelength=> alignment output line length (default 60)

okay so this one makes you a brand new Bio::AlignIO object that handles clustalw files. it returns a Bio::AlignIO::clustalw object and it takes all those args above. note the -file one needs a ">" when you're writing, and -linelength defaults to 60. periodt. 💅

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💫 next_aln 💫

Title   : next_aln
Usage   : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : Bio::Align::AlignI object
Args    : NONE

gives you the next alignment in the stream, as a Bio::Align::AlignI object. Args? NONE. zero. nada. it takes no arguments, it just delivers. 🎁

See Bio::Align::AlignI for details.

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🎀 write_aln 🎀

Title   : write_aln
Usage   : $stream->write_aln(@aln)
Function: writes the clustalw-format object (.aln) into the stream
Returns : 1 for success and 0 for error
Args    : Bio::Align::AlignI object

writes the clustalw-format object (.aln) into the stream. Returns 1 for success and 0 for error — very binary of it, very "we either ate or we didn't". 🔥

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🍓 percentages 🍓

Title   : percentages
Usage   : $obj->percentages($newval)
Function: Set the percentages flag - whether or not to show percentages in
          each output line
Returns : value of percentages
Args    : newvalue (optional)

Set the percentages flag — whether or not to show percentages in each output line. Returns the value of percentages, and the newvalue arg is optional so you can also just peek at it. 👀

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🌈 line_length 🌈

Title   : line_length
Usage   : $obj->line_length($newval)
Function: Set the alignment output line length
Returns : value of line_length
Args    : newvalue (optional)

Set the alignment output line length. Returns the value of line_length, and again the newvalue is optional. lowkey the most chill setter of the bunch. 🧘

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that's the whole page bestie, every option, every arg, every address, nothing skipped, nothing invented. 💖

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this gem of a doc came from perl v5.32.1, dated 2021-08-15, filed under Bio::A...ustalw(3pm) — yes the name got truncated mid-word, it's giving mysterious, it's giving enigma, and we respect it. mwah. 💋