Bio::T...Result(3pm)

🌸 NAME 🌸

Bio::Tools::AnalysisResult — it's the base class for analysis result objects and parsers, bestie. The manual page you're reading is Bio::T...Result(3pm) (they truncate it, it's giving abbreviations), and it lives in the User Contributed Perl Documentation corner of the world.

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✨ SYNOPSIS ✨

# obtain a AnalysisResult derived object somehow

print "Method ", $result->analysis_method(),
      ", version ", $result->analysis_method_version(),
      ", performed on ", $result->analysis_date(), "\n";

# annotate a sequence utilizing SeqAnalysisParserI methods
while($feat = $result->next_feature()) {
    $seq->add_SeqFeature($feat);
}
$result->close();

# query object, e.g. a Bio::SeqI implementing object
$queryseq = $result->analysis_query();

# Subject of the analysis -- may be undefined. Refer to derived module
# to find out what is returned.
$subject = $result->analysis_subject();

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💖 DESCRIPTION 💖

So AnalysisResult is meant to be the base class for modules that wrap up parsers and interpreters for the result of an analysis that got carried out with a query sequence. Main character energy, honestly.

The whole notion of "an analysis" that this base class is working with? It's a unary or binary operator — it takes either one query, or a query and a subject, and produces a result. The query is, like, a sequence (for example), and a subject is either also a sequence, or a database of sequences. Simple as that.

This module also implements the Bio::SeqAnalysisParserI interface, so it can be dropped in anywhere such an object fits. Go look at Bio::SeqAnalysisParserI for that. Devs, you get a ready-to-use parse() method handed to you — but you have to implement next_feature() in whatever class inherits from this. Support for initialization with input file names and reading from streams is also ready to use. Obsessed.

Heads up: this module does not provide support for running an analysis. Not its job, not its vibe. It sits in the subsequent parsing step — the one concerned with turning raw results into BioPerl objects. 🦋

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — literally, it's how the thing grows. 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

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

…rather than to the module maintainer directly. There are lots of experienced and reponsive experts who will be able to look at the problem and quickly address it. If at all possible, please include a thorough description of the problem along with code and data examples. Give them something to work with, bestie. 💅

🐛 Reporting Bugs

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

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

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👑 AUTHOR - Hilmar Lapp 👑

Email: hlapp-at-gmx.net

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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 group chat "do not perceive me" signal, iykyk.

🧚 _initialize_state

• Title: _initialize_state
• Usage: n/a; usually called by _initialize()
• Function: This method is for BioPerl developers only, as indicated by the leading underscore in its name.

Performs initialization or reset of the state of this object. The difference to _initialize() is that it may be called at any time, and repeatedly within the lifetime of this object. Note, however, that this is potentially dangerous in a multi-threading environment. In general, calling this method twice is discouraged for this reason.

This method is supposed to reset the state such that any 'history' is lost. State information that does not change during object lifetime is not considered as history, e.g. parent, name, etc shall not be reset. An inheriting object should only be concerned with state information it introduces itself, and for everything else call SUPER::_initialize_state(@args).

An example is parsing an input file: a state reset implies discarding any unread input, and the actual input itself, followed by setting the new input.

The argument syntax is the same as for new() and _initialize(), i.e., named parameters following the -name=>$value convention. The following parameters are dealt with by the implementation provided here:

-INPUT, -FH, -FILE

(tags are case-insensitive).

• Example:
• Returns:
• Args:

🍓 analysis_query

• Usage: $query_obj = $result->analysis_query();
• Purpose: Set/Get the name of the query used to generate the result — that is, the entity on which the analysis was performed. Will mostly be a sequence object (Bio::PrimarySeq compatible).
• Argument:
• Returns: The object set before. Mostly a Bio::PrimarySeq compatible object.

🦋 analysis_subject

• Usage: $result->analyis_subject();
• Purpose: Set/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: The object that was set before, or undef.
• Argument:

💜 analysis_date

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

⭐ analysis_method

• Usage: $result->analysis_method();
• Purpose: Set/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

🌸 analysis_method_version

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

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And that's the whole page, bestie!! 🎀 This was brought to you by perl v5.32.1, dated 2021-08-15, and it went out under the name Bio::T...Result(3pm). Slay, bye!! 💖✨