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

Bio::Search::Tiling::TilingI 💖

okay bestie, welcome to the manual page for Bio::Search::Tiling::TilingI, a User Contributed Perl Documentation joint, and yes it's giving "abstract interface" energy the whole way through. sit down, grab a strawberry 🍓, we're doing this.

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✨ NAME ✨

Bio::Search::Tiling::TilingI — the abstract interface for an HSP tiling module. it's the vibe, not the implementation. 💅

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🦋 SYNOPSIS 🦋

not used directly, bestie. it's a developer-facing interface, but the POD here is genuinely useful for devs. no cap.

the whole point of the interface is to make this glow-up as painless as possible. watch this.

From (the Bio::Search::SearchUtils-based era):

 # Bio::Search::SearchUtils-based
 while ( local $_ = $result->next_hit ) {
    printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n",
      $hit->significance, $hit->frac_aligned_query, $hit->num_identical);
 }

To (the TilingI-based era, main character energy):

 # TilingI-based
 while ( local $_ = $result->next_hit ) {
    my $tiling = Bio::Search::Tiling::MyTiling($_);
    printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n",
      $hit->significance, $tiling->frac_aligned_query, $tiling->num_identical);
 }

see how little changed? that's the assignment. 🫶

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🌸 DESCRIPTION 🌸

this module hands out strong suggestions for anyone intending to build an HSP tiling object. if your object subclasses TilingI, you should override the methods defined here, following their descriptions below. that's not optional-flavored, that's the whole deal.

also go read the STATISTICS METHODS section, it's got the hints for implementing methods that stay valid across different algorithms and report types. iykyk.

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💌 FEEDBACK 💌

Mailing Lists

user feedback is literally an integral part of the evolution of this module and every other Bioperl module. send your comments and suggestions preferably to the Bioperl mailing list. 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 and support issues to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer. there are so many experienced and responsive experts on the list who will look at your problem and address it fast. if at all possible, include a thorough description of the problem with code and data examples. receipts help everybody. 🧚

Reporting Bugs

report bugs to the Bioperl bug tracking system so the team can keep track of 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 - Mark A. Jensen 👑

Email maj@fortinbras.us

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (you know the one).

STATISTICS METHODS

think of the tiling statistics as the global counterparts to the similar statistics defined for the individual HSPs. so we're prescribing definitions for a bunch of the synonymous methods already defined in Bio::Search::HSP::HSPI. slay.

the tiling statistics must be able to keep track of the coordinate systems that both the query and the subject sequences live in — like, nucleotide or amino acid. this info is typically inferred from the name of the algorithm that ran the original search, which lives in $hit_object->algorithm. here's a table of algorithm info that may be useful (if you trust us):

 algorithm   query on hit   coordinates(q/h)
 ---------   ------------   ---------------
  blastn      dna on dna         dna/dna
  blastp      aa  on aa           aa/aa
  blastx      xna on aa          dna/aa
 tblastn      aa  on xna          aa/dna
 tblastx      xna on xna         dna/dna
   fasta      dna on dna         dna/dna
   fasta      aa  on aa           aa/aa
   fastx      xna on aa          dna/aa
   fasty      xna on aa          dna/aa
  tfasta      aa  on xna          aa/dna
  tfasty      aa  on xna          aa/dna
 megablast    dna on dna         dna/dna

 xna: translated nucleotide data

statistics methods also have to be aware of differences in reporting between the algorithms. hit attributes are not necessarily normalized over all algorithms. devs, please feel free to add examples to the list below. 🙏

NCBI BLAST vs WU-BLAST (AB-BLAST) lengths

the total length of the alignment is reported differently between these two flavors. $hit_object->length() will contain the number in the denominator of the stats line; i.e., 120 in

 Identical = 34/120 Positives = 67/120

NCBI BLAST uses the total length of the query sequence as input by the user (a.k.a. "with gaps"). WU-BLAST uses the length of the query sequence actually aligned by the algorithm (a.k.a. "without gaps").

finally, devs, remember that sequence data may or may not be associated with the HSPs contained in the hit object. this typically depends on whether a full report (e.g., blastall -m0) or a summary (e.g., blastall -m8) was parsed. statistics methods that depend directly on the sequence data will need to check that that data is present. ⭐

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identities

• Title: identities
• Alias: num_identical
• Usage: $num_identities = $tiling->identities()
• Function: return the estimated or exact number of identities in the tiling, accounting for overlapping HSPs 💅
• Example: (none given)
• Returns: number of identical residue pairs
• Args: (none given)

conserved

• Title: conserved
• Alias: num_conserved
• Usage: $num_conserved = $tiling->conserved()
• Function: return the estimated or exact number of conserved sites in the tiling, accounting for overlapping HSPs ✨
• Example: (none given)
• Returns: number of conserved residue pairs
• Args: (none given)

length

• Title: length
• Usage: $max_length = $tiling->length($type)
• Function: return the total number of residues of the subject or query sequence covered by the tiling
• Returns: number of "logical" residues covered
• Args: scalar $type, one of 'hit', 'subject', 'query'

frac_identical

• Title: frac_identical
• Usage: $tiling->frac_identical($type)
• Function: return the fraction of sequence length consisting of identical pairs
• Returns: scalar float
• Args: scalar $type, one of 'hit', 'subject', 'query'
• Note: this method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above)

percent_identity

• Title: percent_identity
• Usage: $tiling->percent_identity($type)
• Function: return the fraction of sequence length consisting of identical pairs as a percentage
• Returns: scalar float
• Args: scalar $type, one of 'hit', 'subject', 'query'

frac_conserved

• Title: frac_conserved
• Usage: $tiling->frac_conserved($type)
• Function: return the fraction of sequence length consisting of conserved pairs
• Returns: scalar float
• Args: scalar $type, one of 'hit', 'subject', 'query'
• Note: this method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above)

percent_conserved

• Title: percent_conserved
• Usage: $tiling->percent_conserved($type)
• Function: return the fraction of sequence length consisting of conserved pairs as a percentage
• Returns: scalar float
• Args: scalar $type, one of 'hit', 'subject', 'query'

frac_aligned

• Title: frac_aligned
• Usage: $tiling->frac_aligned($type)
• Function: return the fraction of input sequence length that was aligned by the algorithm
• Returns: scalar float
• Args: scalar $type, one of 'hit', 'subject', 'query'
• Note: this method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above)

range

• Title: range
• Usage: $tiling->range($type)
• Function: returns the extent of the longest tiling as ($min_coord, $max_coord)
• Returns: array of two scalar integers
• Args: scalar $type, one of 'hit', 'subject', 'query'

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🎀 TILING ITERATORS 🎀

next_tiling

• Title: next_tiling
• Usage: @hsps = $self->next_tiling($type);
• Function: obtain a tiling of HSPs over the $type ('hit', 'subject', 'query') sequence
• Example: (none given)
• Returns: an array of HSPI objects
• Args: scalar $type: one of 'hit', 'subject', 'query', with 'subject' an alias for 'hit'

rewind_tilings

• Title: rewind_tilings
• Usage: $self->rewind_tilings($type)
• Function: reset the next_tilings($type) iterator
• Example: (none given)
• Returns: true on success
• Args: scalar $type: one of 'hit', 'subject', 'query', with 'subject' an alias for 'hit'

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🌈 INFORMATIONAL ACCESSORS 🌈

algorithm

• Title: algorithm
• Usage: $tiling->algorithm
• Function: retrieve the algorithm name associated with the invocant's hit object
• Returns: scalar string
• Args: (none given)

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and that's the whole page bestie, no crumbs left. 💖

okay bye ily, this was perl v5.32.1, dated 2021-08-15, and it ate. periodt. 💅✨🎀