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

✨ NAME ✨

Bio::Location::Fuzzy — bestie, this is the implementation of a Location on a Sequence that has unclear start and/or end locations 🦋

It ships as Bio::L...:Fuzzy(3pm) in the Perl docs, and yes, we're about to read the whole thing together 💅

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🌸 SYNOPSIS 🌸

use Bio::Location::Fuzzy;
my $fuzzylocation = Bio::Location::Fuzzy->new(
                                             -start => '<30',
                                             -end   => 90,
                                             -location_type => '..');

print "location string is ", $fuzzylocation->to_FTstring(), "\n";
print "location is of the type ", $fuzzylocation->location_type, "\n";

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💖 DESCRIPTION 💖

Okay so this module has every method you need to represent a Fuzzy Location — a location that does not have clear start and/or end points. The vibes are intentionally vague. It's giving "somewhere around there" 🌫️

At first it's here to handle features from Genbank/EMBL feature tables that get written like 1^100 (meaning between bases 1 and 100) or <100..300 (meaning it starts somewhere before 100). Advanced implementations of this interface may be able to handle the whole necessary logic of overlaps/intersection/contains/union — main character energy for a data structure, honestly 👑

It was constructed to handle fuzzy locations that can be represented in Genbank/EMBL and Swissprot. Periodt.

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🫶 FEEDBACK 🫶

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. (Yes bestie, code and data examples — do not just say "it's broken" 😭)

🐛 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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👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl-dot-org

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🧚 APPENDIX 🧚

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

• Title: new
• Usage: my $fuzzyloc = Bio::Location::Fuzzy->new( @args);
• Function: (the original leaves this blank, no cap 🙈)
• Returns: (also blank 😭)
• Args:
  • -start => value for start (initialize by superclass)
  • -end => value for end (initialize by superclass)
  • -strand => value for strand (initialize by superclass)
  • -location_type => either ('EXACT','WITHIN','IN-BETWEEN', 'UNCERTAIN') OR ( 1,2,3,4)
  • -start_ext=> extension for start - defaults to 0,
  • -start_fuz= fuzzy code for start can be ('EXACT','WITHIN','BETWEEN','BEFORE','AFTER', 'UNCERTAIN' ) OR a value 1 - 5 corresponding to index+1 above
  • -end_ext=> extension for end - defaults to 0,
  • -end_fuz= fuzzy code for end can be ('EXACT','WITHIN','BETWEEN','BEFORE','AFTER', 'UNCERTAIN') OR a value 1 - 5 corresponding to index+1 above

location_type

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

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🧬 LocationI methods 🧬

length

• Title: length
• Usage: $length = $fuzzy_loc->length();
• Function: Get the length of this location.

Note that the length of a fuzzy location will always depend on the currently active interpretation of start and end. The result will therefore vary for different CoordinatePolicy objects. So like… same object, different policy, different number. Don't come for me 💀

• Returns: an integer
• Args: none

start

• Title: start
• Usage: $start = $fuzzy->start();
• Function: get/set start of this range, handling fuzzy_starts
• Returns: a positive integer representing the start of the location
• Args: start location on set (can be fuzzy point string)

end

• Title: end
• Usage: $end = $fuzzy->end();
• Function: get/set end of this range, handling fuzzy_ends
• Returns: a positive integer representing the end of the range
• Args: end location on set (can be fuzzy string)

min_start

• Title: min_start
• Usage: $min_start = $fuzzy->min_start();
• Function: get/set the minimum starting point
• Returns: the minimum starting point from the contained sublocations
• Args: integer or undef on set

max_start

• Title: max_start
• Usage: my $maxstart = $location->max_start();
• Function: Get/set maximum starting location of feature startpoint
• Returns: integer or undef if no maximum starting point.
• Args: integer or undef on set

start_pos_type

• Title: start_pos_type
• Usage: my $start_pos_type = $location->start_pos_type();
• Function: Get/set start position type.
• Returns: type of position coded as text ('BEFORE','AFTER','EXACT','WITHIN','BETWEEN','UNCERTAIN')
• Args: a string on set

min_end

• Title: min_end
• Usage: my $minend = $location->min_end();
• Function: Get/set minimum ending location of feature endpoint
• Returns: integer or undef if no minimum ending point.
• Args: integer or undef on set

max_end

• Title: max_end
• Usage: my $maxend = $location->max_end();
• Function: Get/set maximum ending location of feature endpoint
• Returns: integer or undef if no maximum ending point.
• Args: integer or undef on set

end_pos_type

• Title: end_pos_type
• Usage: my $end_pos_type = $location->end_pos_type();
• Function: Get/set end position type.
• Returns: type of position coded as text ('BEFORE','AFTER','EXACT','WITHIN','BETWEEN','UNCERTAIN')
• Args: a string on set

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

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. (iykyk — the ones already out there don't retroactively change, bestie 👀)

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

See Bio::Location::CoordinatePolicyI

to_FTstring

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

Not me noticing this one is word-for-word the seq_id docs 💀 I'm just the messenger, I promise — this is literally what the page says.

valid_Location

• Title: valid_Location
• Usage: if ($location->valid_location) {...};
• Function: boolean method to determine whether location is considered valid (has minimum requirements for Simple implementation)
• Returns: Boolean value: true if location is valid, false otherwise
• Args: none

_fuzzypointdecode

• Title: _fuzzypointdecode
• Usage: ($type,$min,$max) = $self->_fuzzypointdecode('<5');
• Function: Decode a fuzzy string.
• Returns: A 3-element array consisting of the type of location, the minimum integer, and the maximum integer describing the range of coordinates this start or endpoint refers to. Minimum or maximum coordinate may be undefined.
  • Returns empty array on fail. 😭
• Args: fuzzypoint string

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And that's the whole page, bestie 🫶 go forth and be fuzzy ✨

Signed off from perl v5.32.1, dated 2021-08-15, in the pages of Bio::L...:Fuzzy(3pm) — slay 💅🌈