Bio::L...cationI(3pm)

💖 Bio::Location::FuzzyLocationI 💖

okay so bestie, gather round, because we're talking about Bio::Location::FuzzyLocationI — the abstract interface of a Location on a Sequence which has unclear start/end location. yes, that whole mouthful. it lives in the User Contributed Perl Documentation part of the perl manual pages, section 3pm. she's a little niche, she's a little abstract, and honestly? iconic.

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✨ NAME ✨

Bio::Location::FuzzyLocationI — the abstract interface of a Location on a Sequence which has unclear start/end location.

like, the location is fuzzy. the vibes are unclear. the coordinates are going through something. 💅

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🌸 SYNOPSIS 🌸

# Get a FuzzyLocationI object somehow
print "Fuzzy FT location string is ", $location->to_FTstring();
print "location is of the type ", $location->loc_type, "\n";

"somehow" is doing a LOT of heavy lifting in that comment but honestly same, we've all been there. 🫶

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🦋 DESCRIPTION 🦋

so this interface encapsulates the necessary methods for representing a Fuzzy Location — one that does not have clear start and/or end points. the whole point.

it will initially serve to handle features from Genbank/EMBL feature tables that are written as 1^100 meaning between bases 1 and 100, or <100..300 meaning it starts somewhere before 100. it's giving "we know roughly where it is but not exactly" energy and we respect it.

advanced implementations of this interface may be able to handle the necessary logic of overlaps/intersection/contains/union. the base version is not out here doing allat — that's for the advanced girlies.

it was constructed to handle fuzzy locations that can be represented in Genbank/EMBL. periodt.

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🎀 FEEDBACK 🎀

user feedback is an integral part of the evolution of this and other Bioperl modules. so like, your opinion actually matters here, no cap. 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 or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. ok so real talk — many experienced and reponsive experts will be able look at the problem and quickly address it. that's the group chat advantage, bestie, you get the whole squad instead of one tired maintainer's DMs. please include a thorough description of the problem with code and data examples if at all possible. we need the receipts. 📎

🐛 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

do it. the maintainers will thank you. ✨

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👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl-dot-org

(that's the classic obfuscated email format, yes, we know, it's giving 2003 and we love her for it)

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that's the secret menu, iykyk. 🙈

🌈 LocationI methods

💜 location_type

Title   : loc_type
Usage   : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
Args    : none

she tells you what kind of location she is. three possible answers, no in-between... well, actually 'IN-BETWEEN' IS one of the answers, which is very funny, but you get me. 🌸

💫 Bio::LocationI methods

Bio::LocationI methods follow

⭐ min_start

Title   : min_start
Usage   : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args    : none

⭐ max_start

Title   : max_start
Usage   : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args    : none

⭐ start_pos_type

Title   : start_pos_type
Usage   : my $start_pos_type = $location->start_pos_type();
Function: Get start position type (ie <,>, ^)
Returns : type of position coded as text
          ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args    : none

⭐ min_end

Title   : min_end
Usage   : my $minend = $location->min_end();
Function: Get minimum ending location of feature endpoint
Returns : integer or undef if no minimum ending point.
Args    : none

⭐ max_end

Title   : max_end
Usage   : my $maxend = $location->max_end();
Function: Get maximum ending location of feature endpoint
Returns : integer or undef if no maximum ending point.
Args    : none

⭐ end_pos_type

Title   : end_pos_type
Usage   : my $end_pos_type = $location->end_pos_type();
Function: Get end position type (ie <,>, ^)
Returns : type of position coded as text
          ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args    : none

⭐ seq_id

Title   : seq_id
Usage   : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id
Args    : [optional] seq_id value to set

getter AND setter, she's versatile, she contains multitudes. 💅

⭐ coordinate_policy

Title   : coordinate_policy
Usage   : $policy = $location->coordinate_policy();
          $location->coordinate_policy($mypolicy); # set may not be possible
Function: Get the coordinate computing policy employed by this object.

          See Bio::Location::CoordinatePolicyI for documentation about
          the policy object and its use.

          The interface *does not* require implementing classes to accept
          setting of a different policy. The implementation provided here
          does, however, allow one to do so.

          Implementors of this interface are expected to initialize every
          new instance with a CoordinatePolicyI object. The implementation
          provided here will return a default policy object if none has
          been set yet. To change this default policy object call this
          method as a class method with an appropriate argument. Note that
          in this case only subsequently created Location objects will be
          affected.

Returns : A Bio::Location::CoordinatePolicyI implementing object.
Args    : On set, a Bio::Location::CoordinatePolicyI implementing object.

ok important note bestie: that # set may not be possible is NOT a joke. the interface does not require implementing classes to accept setting of a different policy. the implementation provided here does allow it, but don't go assuming every implementation will. also — if you change the default policy as a class method, only subsequently created Location objects will be affected. the ones that already exist? they're not getting the memo. 🙈

⭐ to_FTstring

Title   : to_FTstring
Usage   : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args    : none

the moment we've all been waiting for: the FeatureTable string reveal. ✨

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and that's the whole page, bestie!! go forth and handle your fuzzy locations with confidence 🦋

this was pulled from perl v5.32.1, dated 2021-08-15, and it's the Bio::L...cationI(3pm) manual page (yes the header really truncates her name like that, she's mysterious). mwah, slay, bye 💖✨🎀