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

💖 Bio::L...:Split(3pm) 💖

okay bestie, listen. this is the manual page for Bio::Location::Split, which is part of the User Contributed Perl Documentation collection. she's a Perl module. she's giving location-object-with-multiple-locations. she's iconic. let's get into it 🦋

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✨ NAME ✨

Bio::Location::Split — it's an implementation of a Location on a Sequence that has multiple locations, i.e. multiple start/end points. like, a feature that isn't just one tidy little stretch of sequence. she's fragmented. she's complex. we love her 💅

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✨ SYNOPSIS ✨

use Bio::Location::Split;

my $splitlocation = Bio::Location::Split->new();
$splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>1,
                                                           -end=>30,
                                                           -strand=>1));
$splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>50,
                                                           -end=>61,
                                                           -strand=>1));
my @sublocs = $splitlocation->sub_Location();

my $count = 1;
# print the start/end points of the sub locations
foreach my $location ( sort { $a->start <=> $b->start }
                       @sublocs ) {
    printf "sub feature %d [%d..%d]\n",
           $count, $location->start,$location->end, "\n";
    $count++;
}

like, you make a split location, you shove a couple of Bio::Location::Simple objects into it with add_sub_Location, you pull them back out with sub_Location, and then you sort + loop + print. that's the whole vibe ✨

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✨ DESCRIPTION ✨

so this implementation handles locations that span more than one start/end location, or and/or lie on different sequences. she can also work with split locations that care about the specific order of the sublocations ('join'), or ones that don't have a specific order but represent a feature spanning noncontiguous sublocations ('order', 'bond').

⚠️ heads up bestie: the order you add sublocations in may be very important, depending on the specific split location type. for instance, a 'join' must have its sublocations added in the order that one expects to join the sublocations. all the other types get sorted based on the sequence location. so like, order matters for some and not others. iykyk 🎀

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✨ FEEDBACK ✨

user feedback is an integral part of the evolution of this and other Bioperl modules. so like, 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. give them the whole story, bestie, they can handle it 💖

🎀 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

shoutout Jason 👑 (yes the -AT- and _DOT_ are on purpose, that's how they wrote it, don't come for me)

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✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (the underscore ones are like, backstage, don't touch unless you know what you're doing 🫣)

🌸 each_Location

• Title : each_Location
• Usage : @locations = $locObject->each_Location($order);
• Function : conserved function call across Location:: modules — will return an array containing the component Location(s) in that object, regardless if the calling object is itself a single location or one containing sublocations.
• Returns : an array of Bio::LocationI implementing objects
• Args : Optional sort order to be passed to sub_Location()

🌸 sub_Location

• Title : sub_Location
• Usage : @sublocs = $splitloc->sub_Location();
• Function : returns the array of sublocations making up this compound (split) location. those sublocations referring to the same sequence as the root split location will be sorted by start position (forward sort) or end position (reverse sort) and come first (before those on other sequences).

the sort order can be optionally specified or suppressed by the value of the first argument. the default is no sort.

• Returns : an array of Bio::LocationI implementing objects
• Args : Optionally 1, 0, or -1 for specifying a forward, no, or reverse sort order

🌸 add_sub_Location

• Title : add_sub_Location
• Usage : $splitloc->add_sub_Location(@locationIobjs);
• Function : add an additional sublocation
• Returns : number of current sub locations
• Args : list of Bio::LocationI implementing object(s) to add

🌸 splittype

• Title : splittype
• Usage : $splittype = $location->splittype();
• Function : get/set the split splittype
• Returns : the splittype of split feature (join, order)
• Args : splittype to set

🌸 is_single_sequence

• Title : is_single_sequence
• Usage :

if($splitloc->is_single_sequence()) {
    print "Location object $splitloc is split ".
          "but only across a single sequence\n";
}

• Function : determine whether this location is split across a single or multiple sequences.

this implementation ignores (sub-)locations that do not define seq_id(). the same holds true for the root location.

• Returns : TRUE if all sublocations lie on the same sequence as the root location (feature), and FALSE otherwise.
• Args : none

🌸 guide_strand

• Title : guide_strand
• Usage : $str = $loc->guide_strand();
• Function : get/Set the guide strand. of use only if the split type is a 'join' (this helps determine the order of sublocation retrieval)
• Returns : value of guide strand (1, -1, or undef)
• Args : new value (-1 or 1, optional)

---

✨ LocationI methods ✨

🦋 strand

• Title : strand
• Usage : $obj->strand($newval)
• Function : for SplitLocations, setting the strand of the container (this object) is a short-cut for setting the strand of all sublocations.

in get-mode, checks if no sub-location is remote, and if all have the same strand. if so, it returns that shared strand value. otherwise it returns undef.

• Example :
• Returns : on get, value of strand if identical between sublocations (-1, 1, or undef)
• Args : new value (-1 or 1, optional)

🦋 flip_strand

• Title : flip_strand
• Usage : $location->flip_strand();
• Function : flip-flop a strand to the opposite. also sets Split strand to be consistent with the sublocation strands (1, -1 or undef for mixed strand values)
• Returns : None
• Args : None

🦋 start

• Title : start
• Usage : $start = $location->start();
• Function : get the starting point of the first (sorted) sublocation
• Returns : integer
• Args : none

🦋 end

• Title : end
• Usage : $end = $location->end();
• Function : get the ending point of the last (sorted) sublocation
• Returns : integer
• Args : none

🦋 min_start

• Title : min_start
• Usage : $min_start = $location->min_start();
• Function : get the minimum starting point
• Returns : the minimum starting point from the contained sublocations
• 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

🦋 length

• Title : length
• Usage : $len = $loc->length();
• Function : get the length in the coordinate space this location spans
• Example :
• Returns : an integer
• Args : none

🦋 seq_id

• Title : seq_id
• Usage : my $seqid = $location->seq_id();
• Function : get/Set seq_id that location refers to.

we override this here in order to propagate to all sublocations which are not remote (provided this root is not remote either)

• 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.

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

🦋 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 bestie, you made it to the end, you're literally the main character 🌈👑

this was perl v5.32.1, dated 2021-08-15, from Bio::L...:Split(3pm) — the docs really do be truncating the module name like that, not me, i'm just the messenger 🎀

bye pookie, go sort your sublocations 💖✨🦋