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

🌸 NAME 🌸

Bio::Location::Simple — bestie, it's an implementation of a Simple Location on a Sequence. That's the whole vibe. (Yes, this is the Bio::Location::Simple (3pm) manual page, and yes, we are going to have a good time with it.) 🫶

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✨ SYNOPSIS ✨

use Bio::Location::Simple;

my $location = Bio::Location::Simple->new(
    -start  => 1,
    -end    => 100,
    -strand => 1,
);

if( $location->strand == -1 ) {
    printf "complement(%d..%d)\n", $location->start, $location->end;
} else {
    printf "%d..%d\n", $location->start, $location->end;
}

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💅 DESCRIPTION 💅

Okay so this is an implementation of Bio::LocationI whose whole job is managing exact location info on a Sequence. We're talking '22' or '12..15' or '16^17' — that energy. 💖

You can test the type of the location using the length() function () — yes, exactly like that — or you can go straight to location_type(), which can be one of two values: 'EXACT' or 'IN-BETWEEN'. Two options, no more, iconic behaviour honestly.

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🦋 FEEDBACK 🦋

User feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. 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. Lowkey this is the move — many experienced and responsive 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. The more detail, the better the slay. 💅

🔥 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 - Heikki Lehvaslaiho 👑

Email heikki-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 _.

⭐ start ⭐

• Title: start
• Usage: $start = $loc->start();
• Function: get/set the start of this range
• Returns: the start of this range
• Args: optionally allows the start to be set using $loc->start($start)

⭐ end ⭐

• Title: end
• Usage: $end = $loc->end();
• Function: get/set the end of this range
• Returns: the end of this range
• Args: optionally allows the end to be set using $loc->end($start)
• Note: If start is set but end is undefined, this now assumes that start is the same as end but throws a warning (i.e. it assumes this is a possible error). If start is undefined, this now throws an exception.

Not me getting a warning and an exception depending on the situation 😭 read the Note, bestie, it matters.

⭐ strand ⭐

• Title: strand
• Usage: $strand = $loc->strand();
• Function: get/set the strand of this range
• Returns: the strandedness (-1, 0, +1)
• Args: optionally allows the strand to be set using $loc->strand($strand)

⭐ length ⭐

• Title: length
• Usage: $len = $loc->length();
• Function: get the length in the coordinate space this location spans
• Example: (nothing in there, she's mysterious)
• Returns: an integer
• Args: none

⭐ 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 minimum starting point.
• Args: none

⭐ max_start ⭐

• Title: max_start
• Usage: my $maxstart = $location->max_start();
• Function: Get maximum starting location of feature startpoint.

In this implementation this is exactly the same as min_start().

• 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

In this implementation this is exactly the same as min_end().

• 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

⭐ location_type ⭐

• Title: location_type
• Usage: my $location_type = $location->location_type();
• Function: Get location type encoded as text
• Returns: string ('EXACT' or 'IN-BETWEEN')
• Args: 'EXACT' or '..' or 'IN-BETWEEN' or '^'

⭐ is_remote ⭐

• Title: is_remote
• Usage: $is_remote_loc = $loc->is_remote()
• Function: Whether or not a location is a remote location.

A location is said to be remote if it is on a different 'object' than the object which 'has' this location. Typically, features on a sequence will sometimes have a remote location, which means that the location of the feature is on a different sequence than the one that is attached to the feature. In such a case, $loc->seq_id will be different from $feat->seq_id (usually they will be the same).

While this may sound weird, it reflects the location of the kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL feature tables.

• Example: (empty, she said nothing and left)
• Returns: TRUE if the location is a remote location, and FALSE otherwise
• Args: Value to set to

⭐ to_FTstring ⭐

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

⭐ 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

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okay that's the whole page, you ate that 💜 This was Bio::Location::Simple, rendered for perl v5.32.1, dated 2021-08-15 — go forth and locate things, bestie, you've got this 🦋✨