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

✨ Bio::A...::proda(3pm) — the manual, but make it fashion ✨

okay bestie, so this is the page for Bio::A...::proda(3pm), a Bioperl joint, and it's literally just the vibe guide for Bio::AlignIO::proda. let's get into it 💅

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🌸 NAME 🌸

Bio::AlignIO::proda — the proda sequence input/output stream, periodt.

This gives you the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu). no cap.

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🦋 SYNOPSIS 🦋

Do not use this module directly. like, don't. use it via the Bio::AlignIO class instead, iykyk.

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💜 DESCRIPTION 💜

This object can transform Bio::Align::AlignI objects to and from proda files. that's the whole personality. iconic behavior honestly.

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🫶 FEEDBACK 🫶

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. send your comments and suggestions preferably to one of the Bioperl mailing lists. 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 to the module maintainer directly. Many experienced and reponsive experts will be able 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. give them the full tea 🍵

🐛 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 - Albert Vilella 👑

Email: avilella-at-gmail-dot-com

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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 little secret handshake, bestie).

🌟 new

Title   : new
Usage   : $alignio = Bio::AlignIO->new(-format => 'proda',
                      -file => 'filename');
Function: returns a new Bio::AlignIO object to handle proda files
Returns : Bio::AlignIO::proda 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 (proda only)
          -linelength=> alignment output line length (default 60)

so new builds you a fresh Bio::AlignIO object that handles proda files. give it a -file (add a ">" if you're writing, btw) or a -fh if you'd rather hand over a filehandle directly. -format says what alignment format you're processing or producing. -percentages shows a percentage of identity in each line of the alignment — and that one's proda only, noted. -linelength sets your alignment output line length and defaults to 60. and -verbose takes a verbosity setting of -1, 0, 1, or 2. 💖

🌟 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. no args, she just knows. See Bio::Align::AlignI for details.

🌟 write_aln

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

writes the proda-format object (.aln) into the stream. returns 1 for success and 0 for error — the classic glow-up-or-flop binary. takes a Bio::Align::AlignI object.

🌟 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)

sets the percentages flag — whether or not to show percentages in each output line. returns the value of percentages. the newvalue is optional, so you can also just peek at her 👀

🌟 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)

sets the alignment output line length. returns the value of line_length. newvalue optional, as always.

🌟 no_header

Title   : no_header
Usage   : $obj->no_header($newval)
Function: Set if the alignment input has a CLUSTAL header or not
Returns : value of no_header
Args    : newvalue (optional)

sets if the alignment input has a CLUSTAL header or not. returns the value of no_header. newvalue optional — you already knew that though, bestie 💅

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ok that's the whole page, every last flag and method accounted for, nothing skipped. slay. 🔥

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and that's a wrap! this page was served up by perl v5.32.1, dated 2021-08-15, and it's giving Bio::A...::proda(3pm) main character energy. go forth and align, gorgeous 🌸💖✨