Bio::A...IO::arp(3pm)

💖 Bio::A...IO::arp — bestie edition 💖

okay so this is the manpage for Bio::A...IO::arp, aka the ARP MSA Sequence input/output stream, from the User Contributed Perl Documentation. it lives in the 3pm section (perl module docs, iykyk). sit down, grab a snack, we're doing this 💅

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✨ NAME ✨

Bio::AlignIO::arp — ARP MSA Sequence input/output stream. that's it, that's the whole name, slay 🎀

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✨ SYNOPSIS ✨

okay so literally the first thing you need to know:

Do not use this module directly. use it via the Bio::AlignIO class. no cap. it's a behind-the-scenes girly, not a main character you call up yourself 🫶

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✨ DESCRIPTION ✨

so this object can create Bio::SimpleAlign objects out of ARP flat files. and what are those? they're typically configuration-like data files for the program Arlequin ✨. if you want more info, go here:

http://lgb.unige.ch/arlequin/

for the moment, this retains the allele sequence data in the DATA section and inserts them into SimpleAlign objects. and bestie, real talk: ARP files that contain other data (RFLP, etc.) are not expected to parse properly. also, if the DNA data is actually SNP data, then the LocatableSeq object instantiation will throw an error 😭 so like. be aware.

this is now set up as a generic parser (i.e. it parses everything) and collects as much data as possible into the SimpleAlign object. here's the general mapping of where data can be found, bestie, study it 📖:

Tag        SimpleAlign
           Method
----------------------------------------------------------------------
Title      description
SampleName id
----------------------------------------------------------------------

and then, for the annotation girlies:

Tag        Bio::Annotation   TagName                    Bio::Annotation
           Class                                        Parameters
----------------------------------------------------------------------
 NE        SimpleValue       pfam_family_accession      value
 NL        SimpleValue       sequence_start_stop        value
 SS        SimpleValue       sec_structure_source       value
 BM        SimpleValue       build_model                value
 RN        Reference         reference                  *
----------------------------------------------------------------------
* RN is generated based on the number of Bio::Annotation::Reference objects

in addition, the number of samples found in the alignment is retained in a Bio::Annotation::TagTree object in the annotation collection, and it's accessible via this iconic little snippet:

($samples) = $aln->annotation->get_Annotations('Samples');
say $samples->display_text;
# or use other relevant TagTree methods to retrieve data

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🌸 FEEDBACK 🌸

💌 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 responsive experts will be able look at the problem and quickly address it. and please include a thorough description of the problem with code and data examples if at all possible — give them the receipts, bestie 🧾💖

🐛 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 👑

Chris Fields (cjfields) — the icon, the moment, the legend ✨

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🦋 APPENDIX 🦋

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (so if you see an underscore, mind your business, that's internal ✋).

🌈 next_aln

• Title — next_aln
• Usage — $aln = $stream->next_aln
• Function — returns the next alignment in the stream.
• Returns — Bio::Align::AlignI object — returns 0 on end of file or on error
• Args — -width => optional argument to specify the width sequence will be written (60 chars by default)

See Bio::Align::AlignI

🌈 write_aln

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

See Bio::Align::AlignI

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and that's the whole page, periodt 💅✨

this was perl v5.32.1, dated 2021-08-15, and it's filed under Bio::A...IO::arp(3pm) in the User Contributed Perl Documentation — mwah, go forth and parse responsibly 🫶🎀💖