Bio::S...leUtils(3pm)

💖 NAME 💖

okay so welcome to Bio::S...leUtils(3pm), bestie — full name on the tin is Bio::Search::Tiling::MapTileUtils, and it's a little utility drawer full of helpers for manipulating closed intervals for an HSP tiling algorithm. that's the whole vibe. 🧚

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✨ SYNOPSIS ✨

Not used directly.

🦋 DESCRIPTION 🦋

Not used directly.

like, genuinely — you don't call this one yourself. it's the backstage crew. 💅

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🌸 NOTE 🌸

An "interval" in this module is defined as an arrayref [$a0, $a1], where $a0, $a1 are scalar numbers satisfying $a0 <= $a1.

so like, ordered. smallest first. don't come in here with your chaos intervals. 😌

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👑 AUTHOR 👑

Mark A. Jensen - maj -at- fortinbras -dot- us

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🎀 APPENDIX 🎀

all the functions, one by one, no skipping, periodt.

🍓 interval_tiling

• Title: interval_tiling()
• Usage: @tiling = interval_tiling( \@array_of_intervals )
• Function: Find minimal set of intervals covering the input set
• Returns: array of arrayrefs of the form

( [$interval => [ @indices_of_collapsed_input_intervals ]], ...)

• Args: arrayref of intervals

💜 decompose_interval

• Title: decompose_interval
• Usage: @decomposition = decompose_interval( \@overlappers )
• Function: Calculate the disjoint decomposition of a set of overlapping intervals, each annotated with a list of covering intervals
• Returns: array of arrayrefs of the form

( [[@interval] => [@indices_of_coverers]], ... )

• Args: arrayref of intervals (arrayrefs like [$a0, $a1], with
• Note: Each returned interval is associated with a list of indices of the original intervals that cover that decomposition component (scalar size of this list could be called the 'coverage coefficient')
• Note: Coverage: each component of the decomp is completely contained in the input intervals that overlap it, by construction.
• Caveat: This routine expects the members of @overlappers to overlap, but doesn't check this.

okay bestie real talk: that Args line literally just trails off at "with" in the original and i am NOT about to invent the rest, no cap 😭 and the Caveat is a real one — it expects overlap and never verifies it, so if you hand it non-overlapping stuff that's on you. 🙈

🦋 are_disjoint

• Title: are_disjoint
• Usage: are_disjoint( [$a0, $a1], [$b0, $b1] )
• Function: Determine if two intervals are disjoint
• Returns: True if the intervals are disjoint, false if they overlap
• Args: array of two intervals

⭐ min_covering_interval

• Title: min_covering_interval
• Usage: $interval = min_covering_interval( [$a0,$a1],[$b0,$b1] )
• Function: Determine the minimal covering interval for two intervals
• Returns: an interval
• Args: two intervals

🌈 get_intervals_from_hsps

• Title: get_intervals_from_hsps
• Usage: @intervals = get_intervals_from_hsps($type, @hsp_objects)
• Function: Return array of intervals of the form [ $start, $end ], from an array of hsp objects
• Returns: an array of intervals
• Args: scalar $type, array of HSPI objects; where $type is one of 'hit', 'subject', 'query'

💅 _allowable_filters

• Title: _allowable_filters
• Usage: _allowable_filters($Bio_Search_Hit_HitI, $type)
• Function: Return the HSP filters (strand, frame) allowed, based on the reported algorithm
• Returns: String encoding allowable filters:
  • s = strand, f = frame
  • Empty string if no filters allowed
  • undef if algorithm unrecognized
• Args: A Bio::Search::Hit::HitI object, scalar $type, one of 'hit', 'subject', 'query'; default is 'query'

🧚 _set_attributes

• Title: _set_attributes
• Usage: $tiling->_set_attributes()
• Function: Sets attributes for invocant that depend on algorithm name
• Returns: True on success
• Args: none
• Note: setting based on the configuration table %alg_lookup

🌸 containing_hsps()

• Title: containing_hsps
• Usage: @hsps = containing_hsps($interval, @hsps_to_search)
• Function: Return a list of hsps whose coordinates completely contain the given $interval
• Returns: Array of HSP objects
• Args: $interval : [$int1, $int2], array of HSP objects

👑 covering_groups()

• Title: covering_groups
• Usage: (empty in the original, bestie — nothing to copy 💀)
• Function: divide a list of ordered,disjoint intervals (as from a coverage map) into a set of disjoint covering groups
• Returns: array of arrayrefs, each arrayref a covering set of intervals
• Args: array of intervals

🔥 matches_MT

• Title: matches_MT
• Usage: $hsp->matches($type, $action, $start, $end)
• Purpose: Get the total number of identical or conserved matches in the query or sbjct sequence for the given HSP. Optionally can report data within a defined interval along the seq.
• Returns: scalar int
• Args: (nothing listed 💅)
• Comments: Relies on seq_str('match') to get the string of alignment symbols between the query and sbjct lines which are used for determining the number of identical and conservative matches.
• Note: Modeled on Bio::Search::HSP::HSPI::matches

🎀 get_SeqFeatures

• Title: get_SeqFeatures
• Usage: (empty 💀)
• Function: Get the feature objects held by this feature holder.

Features which are not top-level are subfeatures of one or more of the returned feature objects, which means that you must traverse the subfeature arrays of each top-level feature object in order to traverse all features associated with this sequence.

Top-level features can be obtained by tag, specified in the argument.

Use get_all_SeqFeatures() if you want the feature tree flattened into one single array.

• Example: (empty)
• Returns: an array of Bio::SeqFeatureI implementing objects
• Args: [optional] scalar string (feature tag)

🫶 feature_count

• Title: feature_count
• Usage: $seq->feature_count()
• Function: Return the number of SeqFeatures attached to a sequence
• Returns: integer representing the number of SeqFeatures
• Args: None

💜 add_SeqFeature

• Title: add_SeqFeature
• Usage:

$seq->add_SeqFeature($feat);
$seq->add_SeqFeature(@feat);

• Function: Adds the given feature object (or each of an array of feature objects to the feature array of this sequence. The object passed is required to implement the Bio::SeqFeatureI interface.
• Returns: 1 on success
• Args: A Bio::SeqFeatureI implementing object, or an array of such objects.

🦋 remove_SeqFeatures

• Title: remove_SeqFeatures
• Usage: $seq->remove_SeqFeatures();
• Function: Flushes all attached SeqFeatureI objects.

To remove individual feature objects, delete those from the returned array and re-add the rest.

• Example: (empty)
• Returns: The array of Bio::SeqFeatureI objects removed from this seq.
• Args: None

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and that's the whole page, bestie 💖 this one shipped as User Contributed Perl Documentation for Bio::S...leUtils(3pm), built against perl v5.32.1 and dated 2021-08-15. slay, go tile some intervals, i'm obsessed 🎀✨