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

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 Bio::S...delHSP(3pm) 💖

okay so bestie, welcome to the manpage for Bio::S...delHSP(3pm) — User Contributed Perl Documentation era. let's get into it ✨

✨ NAME ✨

Bio::Search::HSP::ModelHSP — a HSP object for model-based searches 💅

🌸 SYNOPSIS 🌸

use Bio::Search::HSP::ModelHSP;
# us it just like a Bio::Search::HSP::ModelHSP object

literally just use it and go, no cap 🫶

🦋 DESCRIPTION 🦋

okay so</purl> this object is a specialization of Bio::Search::HSP::ModelHSP, and it's the one you reach for when your search involves a query model instead of a plain old sequence. we're talking:

  • a Hidden Markov Model (HMM) 👑
  • a covariance model (CM) 🌸
  • a descriptor ✨
  • or literally anything else besides a sequence 💀
vibe check / warning: any results coming from HSPI class methods that assume the query is a sequence? unreliable, bestie. 😭 they've been overridden with warnings saying they haven't been implemented at this time. so like… don't trust those numbers, fr fr. 🙈

💬 FEEDBACK 💬

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, they genuinely want to hear from you. send your comments and suggestions preferably to the Bioperl mailing list. 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. because the way that 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. the more detail the better, iykyk ✨

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so they can keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

go off, file that issue 🎀

👑 AUTHOR - Chris Fields 👑

Email cjfields at bioperl dot org 💌

🦋 APPENDIX 🦋

okay bestie, this is the deep-dive part 💅 the rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — that underscore is basically the "backstage pass only" marker, iykyk 🎀

🌸 new 🌸

  • Title: new
  • Usage: my $obj = Bio::Search::HSP::ModelHSP->new();
  • Function: Builds a new Bio::Search::HSP::ModelHSP object — brand new baby HSP, fresh out the box ✨
  • Returns: Bio::Search::HSP::ModelHSP
  • Args:

Plus Bio::Seach::HSP::ModelHSP methods, and here's the full menu of things you can hand it 🍓:

  • -algorithm => algorithm used (Infernal, RNAMotif, ERPIN, etc)
  • -evalue => evalue
  • -pvalue => pvalue
  • -bits => bit value for HSP
  • -score => score value for HSP (typically z-score but depends on analysis)
  • -hsp_length => Length of the HSP (including gaps)
  • -identical => # of residues that that matched identically
  • -conserved => # of residues that matched conservatively (only protein comparisons; conserved == identical in nucleotide comparisons)
  • -hsp_gaps => # of gaps in the HSP
  • -query_gaps => # of gaps in the query in the alignment
  • -hit_gaps => # of gaps in the subject in the alignment
  • -query_name => HSP Query sequence name (if available)
  • -query_start => HSP Query start (in original query sequence coords)
  • -query_end => HSP Query end (in original query sequence coords)
  • -hit_name => HSP Hit sequence name (if available)
  • -hit_start => HSP Hit start (in original hit sequence coords)
  • -hit_end => HSP Hit end (in original hit sequence coords)
  • -hit_length => total length of the hit sequence
  • -query_length => total length of the query sequence
  • -query_seq => query sequence portion of the HSP
  • -hit_seq => hit sequence portion of the HSP
  • -homology_seq => homology sequence for the HSP
  • -hit_frame => hit frame (only if hit is translated protein)
  • -query_frame => query frame (only if query is translated protein)
  • -meta => optional meta data (sec structure, markup, etc)
  • -custom_score => custom score data

🎀 meta 🎀

  • Title: meta
  • Usage: my $meta = $hsp->meta();
  • Function: Returns meta data for this HSP or undef
  • Returns: string of meta data or undef
  • Args: [optional] string to set value
  • Note: At some point very soon this will likely be a Bio::AnnotationI. Don't get used to a simple string!
🚨 fr fr listen up: do not build your whole life around this being a plain string. The glow-up to Bio::AnnotationI is imminent, so enjoy the simple era while it lasts 😭

🌈 noncanonical_string 🌈

  • Title: noncanonical_string
  • Usage: my $nc_seq = $hsp->noncanonical_string();
  • Function: Returns noncanonical string (NC) data for this HSP or undef
  • Returns: string of noncanonical data or undef
  • Args: [optional] string to set value

💜 custom_score 💜

  • Title: custom_score
  • Usage: my $data = $hsp->custom_score();
  • Function: Returns custom_score data for this HSP, or undef
  • Returns: custom_score data or undef
  • Args: [optional] custom_score
  • Note: This is a Get/Set used to deal with odd score-like data generated from RNAMotif (and other programs) where the score section can be customized to include non-standard data, including sequence data, user-based scores, and other values.

⭐ Bio::Search::HSP::HSPI methods ⭐

Implementation of Bio::Search::HSP::HSPI methods follow 👑

🧚 algorithm 🧚

  • Title: algorithm
  • Usage: my $r_type = $hsp->algorithm
  • Function: Obtain the name of the algorithm used to obtain the HSP
  • Returns: string (e.g., BLASTP)
  • Args: [optional] scalar string to set value

🦋 strand 🦋

  • Title: strand
  • Usage: $hsp->strand('hit')
  • Function: Retrieves the strand for the HSP component requested
  • Returns: +1 or -1 (0 if unknown)
  • Args: 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject. There is no strand available for 'query', as the query is a model and not a true sequence.
bestie the query is a model, not a real sequence, so it has no strand. It's giving main character energy without a physical form 💀

💖 seq 💖

  • Usage: $hsp->seq( [seq_type] );
  • Purpose: Get the query or sbjct sequence as a Bio::Seq.pm object.
  • Example: $seqObj = $hsp->seq('sbjct');
  • Returns: Object reference for a Bio::Seq.pm object.
  • Argument: seq_type = 'query' or 'hit' or 'sbjct' (default = 'sbjct').
    • ('sbjct' is synonymous with 'hit')
    • default is 'sbjct'
    • Note: if there is no sequence available (eg for a model-based search), this returns a LocatableSeq object w/o a sequence
  • Throws: Propagates any exception that occurs during construction of the Bio::Seq.pm object.
  • Comments: The sequence is returned in an array of strings corresponding to the strings in the original format of the Blast alignment. (i.e., same spacing).
  • See Also: seq_str(), Bio::Seq

🍓 pvalue 🍓

  • Title: pvalue
  • Usage: my $pvalue = $hsp->pvalue();
  • Function: Returns the P-value for this HSP or undef
  • Returns: float or exponential (2e-10)
    • P-value is not defined with NCBI Blast2 reports.
  • Args: [optional] numeric to set value

✨ evalue ✨

  • Title: evalue
  • Usage: my $evalue = $hsp->evalue();
  • Function: Returns the e-value for this HSP
  • Returns: float or exponential (2e-10)
  • Args: [optional] numeric to set value

🌸 gaps 🌸

  • Title: gaps
  • Usage: my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
  • Function: Get the number of gaps in the query, hit, or total alignment.
  • Returns: Integer, number of gaps or 0 if none
  • Args:
    • arg 1: 'query' = num gaps in query seq, 'hit' = num gaps in hit seq, 'total' = num gaps in whole alignment, default = 'total'
    • arg 2: [optional] integer gap value to set for the type requested

🎀 query_string 🎀

  • Title: query_string
  • Usage: my $qseq = $hsp->query_string;
  • Function: Retrieves the query sequence of this HSP as a string
  • Returns: string
  • Args: [optional] string to set for query sequence

💅 hit_string 💅

  • Title: hit_string
  • Usage: my $hseq = $hsp->hit_string;
  • Function: Retrieves the hit sequence of this HSP as a string
  • Returns: string
  • Args: [optional] string to set for hit sequence

🫶 homology_string 🫶

  • Title: homology_string
  • Usage: my $homo_string = $hsp->homology_string;
  • Function: Retrieves the homology sequence for this HSP as a string.
    • The homology sequence is the string of symbols in between the query and hit sequences in the alignment indicating the degree of conservation (e.g., identical, similar, not similar).
  • Returns: string
  • Args: [optional] string to set for homology sequence

🔥 length 🔥

  • Title: length
  • Usage: my $len = $hsp->length( ['query'|'hit'|'total'] );
  • Function: Returns the length of the query or hit in the alignment (without gaps) or the aggregate length of the HSP (including gaps; this may be greater than either hit or query )
  • Returns: integer
  • Args:
    • arg 1: 'query' = length of query seq (without gaps), 'hit' = length of hit seq (without gaps), 'total' = length of alignment (with gaps), default = 'total'
    • arg 2: [optional] integer length value to set for specific type

🌈 frame 🌈

  • Title: frame
  • Usage: my ($qframe, $hframe) = $hsp->frame('list',$queryframe,$subjectframe)
  • Function: Set the Frame for both query and subject and insure that they agree. This overrides the frame() method implementation in FeaturePair.
  • Returns: array of query and subject frame if return type wants an array, or query frame if defined or subject frame if not defined
  • Args: 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default), 'query' to retrieve the query frame, 'list' or 'array' to retrieve both query and hit frames together
  • Note: Frames are stored in the GFF way (0-2) not 1-3 as they are in BLAST (negative frames are deduced by checking the strand of the query or hit)
⚠️ not me stressing about frame math: GFF says 0-2, BLAST says 1-3, and negative frames get deduced from the strand of the query or hit. Keep those straight or your alignment will be in shambles 😭

👑 get_aln 👑

  • Title: get_aln
  • Usage: my $aln = $hsp->gel_aln
  • Function: Returns a Bio::SimpleAlign representing the HSP alignment
  • Returns: Bio::SimpleAlign
  • Args: none

💖 Inherited from Bio::SeqFeature::SimilarityPair 💖

These methods come from Bio::SeqFeature::SimilarityPair — freebies, handed down like vintage 🎁

🦋 query 🦋

  • Title: query
  • Usage: my $query = $hsp->query
  • Function: Returns a SeqFeature representing the query in the HSP
  • Returns: Bio::SeqFeature::Similarity
  • Args: [optional] new value to set

🌸 hit 🌸

  • Title: hit
  • Usage: my $hit = $hsp->hit
  • Function: Returns a SeqFeature representing the hit in the HSP
  • Returns: Bio::SeqFeature::Similarity
  • Args: [optional] new value to set

✨ significance ✨

  • Title: significance
  • Usage: $evalue = $obj->significance(); $obj->significance($evalue);
  • Function: Get/Set the significance value
  • Returns: numeric
  • Args: [optional] new value to set

🍓 score 🍓

  • Title: score
  • Usage: my $score = $hsp->score();
  • Function: Returns the score for this HSP or undef
  • Returns: numeric
  • Args: [optional] numeric to set value

⭐ bits ⭐

  • Title: bits
  • Usage: my $bits = $hsp->bits();
  • Function: Returns the bit value for this HSP or undef
  • Returns: numeric
  • Args: none

🚫 ModelHSP methods overridden in ModelHSP 🚫

The following methods have been overridden due to their current reliance on sequence-based queries. They may be implemented in future versions of this class.

🙈 no cap, these are currently overridden because they were all built assuming sequence-based queries. They might get implemented in future versions of this class — until then, don't count on them bestie.
  • seq_inds
  • frac_identical
  • frac_conserved
  • matches
  • num_conserved
  • num_identical
  • cigar_string
  • generate_cigar_string
  • percent_identity

and that's the whole page, bestie 🫶 you made it to the end, which is genuinely iconic of you 💅 this was perl v5.32.1, dated 2021-08-15 — so yes, this lore is from a minute ago, but the knowledge still slaps ✨ go forth and align something beautiful 🌸🦋

📦 where this page comes from