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

💖 Bio::AnalysisResultI 💖

okay bestie, so you found the manual page for Bio::AnalysisResultI, which lives in the User Contributed Perl Documentation corner of the Perl universe, and honestly? it's giving "interface, not a vibe you can instantiate." let's get into it 🦋

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✨ NAME ✨

Bio::AnalysisResultI — the interface for analysis result objects. that's it, that's the whole name. short, sweet, iconic 👑

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🌸 SYNOPSIS 🌸

Bio::AnalysisResultI defines an interface that must be implemented by a
subclass. So you cannot create Bio::AnalysisResultI objects, only
objects that inherit from Bio::AnalysisResultI.

no cap, you literally cannot make a Bio::AnalysisResultI object yourself. it's a blueprint, a mood board, a set of rules. you gotta inherit from it, bestie. that's the whole assignment. 💅

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🎀 DESCRIPTION 🎀

so the AnalysisResultI module is out here providing an interface for modules that wrap up the result of an analysis — and that analysis was run with a query sequence and an optional subject dataset. two ingredients, one of them optional. very flexible of it. ✨

the notion of an analysis that this base class is representing is that of a unary or binary operator — meaning it either takes one query, or a query plus a subject, and then produces a result. so like: the query is, for example, a sequence. and a subject is either a sequence too, or a database of sequences. simple as that. 🌈

this interface defines methods to access analysis result data, and it does not impose any constraints on how that analysis result data is acquired. it's not nosy like that. it doesn't care where the data came from, only that you can get to it. 🫶

🚨 important aside: this module does not provide support for running an analysis. nope. it is positioned in the subsequent parsing step — the part concerned with turning raw results into BioPerl objects. it's the glow-up phase, not the workout. 💀

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💬 FEEDBACK 💬

📬 Mailing Lists

user feedback is an integral part of the evolution of this module and other Bioperl modules — like, genuinely, your comments and suggestions matter. send them 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

okay so if you've got a usage question or a support issue, please direct it to the mailing list:

bioperl-l@bioperl.org

rather than sliding into the module maintainer's DMs directly. why? because there are many experienced and responsive experts on the list who can look at your problem and address it quickly. group chat >> private message, always. 👑

and please include a thorough description of the problem, with code and data examples if at all possible. the more context, the faster the fix. periodt. 💅

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system — it helps everyone keep track of the bugs and their resolutions. bug reports can be submitted via the web at:

https://github.com/bioperl/bioperl-live/issues

go forth and file. it's a public service and it's lowkey iconic of you. 🦋

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👑 AUTHOR - Steve Chervitz, Hilmar Lapp 👑

Email sac@bioperl.org

Email hlapp@gmx.net (author of Bio::Tools::AnalysisResult on which this module is based)

shoutout to the original blueprint, Bio::Tools::AnalysisResult. the ancestors ate. 🍓

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©️ COPYRIGHT ©️

Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

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🙈 DISCLAIMER 🙈

This software is provided "as is" without warranty of any kind.

like, no warranty. none. zero. not even a little one. we said what we said. 😭

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with an _ — that underscore is the "do not perceive me" of Perl. 🙈

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🔍 analysis_query

• Usage: $query_obj = $result->analysis_query();
• Purpose: Get a Bio::PrimarySeqI-compatible object representing the entity on which the analysis was performed. Lacks sequence information.
• Argument: n/a
• Returns: A Bio::PrimarySeqI-compatible object without sequence information. The sequence will have display_id, description, moltype, and length data.

so you get the entity the analysis ran on — but heads up, it has no sequence info. it's the ID card, not the whole person. you still get display_id, description, moltype, and length though. 💖

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🔍 analysis_subject

• Usage: $obj = $result->analyis_subject();
• Purpose: Get the subject of the analysis against which it was performed. For similarity searches it will probably be a database, and for sequence feature predictions (exons, promoters, etc) it may be a collection of models or homologous sequences that were used, or undefined.
• Returns: An object of a type the depends on the implementation. May also return undef for analyses that don't involve subjects.
• Argument: n/a
• Comments: Implementation of this method is optional. AnalysisResultI provides a default behavior of returning undef.

ngl, implementing this one is optional, and the default behavior is just returning undef. sometimes the answer is "no subject, bestie." that's valid. 🫶

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🔍 analysis_subject_version

• Usage: $vers = $result->analyis_subject_version();
• Purpose: Get the version string of the subject of the analysis.
• Returns: String or undef for analyses that don't involve subjects.
• Argument: n/a
• Comments: Implementation of this method is optional. AnalysisResultI provides a default behavior of returning undef.

same energy as above: optional, and the fallback is undef. it's giving "not my department unless you say so." 💅

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📅 analysis_date

• Usage: $date = $result->analysis_date();
• Purpose: Get the date on which the analysis was performed.
• Returns: String
• Argument: n/a

when did this happen? now you know. time is a construct but this method is not. ⭐

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🧪 analysis_method

• Usage: $meth = $result->analysis_method();
• Purpose: Get the name of the sequence analysis method that was used to produce this result (BLASTP, FASTA, etc.). May also be the actual name of a program.
• Returns: String
• Argument: n/a

BLASTP, FASTA, etc. — or literally just the name of the program. either way you get a String back. no notes. 🔥

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🧪 analysis_method_version

• Usage: $vers = $result->analysis_method_version();
• Purpose: Get the version string of the analysis program.
• (e.g., 1.4.9MP, 2.0a19MP-WashU).
• Returns: String
• Argument: n/a

yes those are real version strings. 1.4.9MP and 2.0a19MP-WashU are out here looking like wifi passwords and we respect them. 🌈

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🦋 next_feature

• Title: next_feature
• Usage: $seqfeature = $obj->next_feature();
• Function: Returns the next feature available in the analysis result, or undef if there are no more features.
• Example:
• Returns: A Bio::SeqFeatureI implementing object, or undef if there are no more features.
• Args: none

call it in a loop, get features one at a time, and when it hands you undef? that's the finale. no more features, show's over, take a bow. 🎀

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and that's the whole page, bestie!! you understood the assignment 💅✨

this lil manual page came to you courtesy of perl v5.32.1, dated 2021-08-15, under the manual name Bio::A...esultI(3pm) — go forth and implement that interface, you gorgeous main character 🫶💖🦋