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

💖 Bio::Search::HSP::HMMERHSP 💖

okay bestie, so the manual page header here is Bio::S...MERHSP(3pm) — that's the User Contributed Perl Documentation version, and yes the title got the classic manpage squeeze. We're talking about Bio::Search::HSP::HMMERHSP today and honestly? she's a specialist. 👑

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✨ NAME ✨

Bio::Search::HSP::HMMERHSP — an HSP object built for HMMER results 🧬

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🌸 SYNOPSIS 🌸

okay so here's the vibe, literally just:

use Bio::Search::HSP::HMMERHSP;
# use it just like a Bio::Search::HSP::GenericHSP object

that's it. that's the whole entrance. no secret handshake. 🫶

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🦋 DESCRIPTION 🦋

so Bio::Search::HSP::HMMERHSP is a specialization of Bio::Search::HSP::GenericHSP. like, she inherited the whole family personality and then went and made it HMMER-specific. it's giving nepo baby but make it useful, iykyk. 💅

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

user feedback is, like, an integral part of the evolution of this module and all the other Bioperl modules, no cap. so if you've got comments or suggestions, pls pls send them to the Bioperl mailing list. your participation is so much appreciated, fr fr. 🥹

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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🫶 Support 🫶

okay important: for usage questions and support issues, direct them to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, bestie. there are so many experienced and responsive experts on there who can look at your problem and get it addressed quickly. 🙈

if at all possible, pls include a thorough description of the problem along with code and data examples. the more context you give, the faster someone can help you out. 💖

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🐛 Reporting Bugs 🐛

found a bug? report it to the Bioperl bug tracking system so they can actually keep track of the bugs and their resolutions. you can submit bug reports via the web at:

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

go off, be the hero. 🔥

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👑 AUTHOR - Jason Stajich 👑

Email: jason-at-bioperl.org ✨

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more parts incoming, don't go anywhere 💜

🌈 APPENDIX 🌈

okay bestie the main event is done but there's SO much more. the rest of this documentation spills every single object method detail. and heads up: internal methods usually start with an underscore _ so you can spot them like a little name tag 👀

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🫶 new

• Title — new
• Usage — my $obj = Bio::Search::HSP::HMMERHSP->new();
• Function — Builds a new Bio::Search::HSP::HMMERHSP object
• Returns — Bio::Search::HSP::HMMERHSP
• Args — (nothing, it's giving low-maintenance ✨)

Plus Bio::Search::HSP::GenericHSP methods, and here's the whole arg menu, verbatim, no substitutions:

-algorithm    => algorithm used (BLASTP, TBLASTX, FASTX, 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)

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✨ Bio::Search::HSP::HSPI methods ✨

Implementation of Bio::Search::HSP::HSPI methods follow, babes. all of them. let's go 💅

🌸 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

🦋 pvalue

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

⚠️ real talk: P-value is not defined with NCBI Blast2 reports. it's just not there, don't come for her 💀

🎀 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

💜 frac_identical

• Title — frac_identical
• Usage — my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
• Function — Returns the fraction of identitical positions for this HSP
• Returns — Float in range 0.0 -> 1.0
• Args —
  • arg 1:
    • 'query' = num identical / length of query seq (without gaps)
    • 'hit' = num identical / length of hit seq (without gaps)
    • 'total' = num identical / length of alignment (with gaps)
    • default = 'total'
  • arg 2: [optional] frac identical value to set for the type requested

🍓 frac_conserved

• Title — frac_conserved
• Usage — my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
• Function — Returns the fraction of conserved positions for this HSP. This is the fraction of symbols in the alignment with a positive score.
• Returns — Float in range 0.0 -> 1.0
• Args —
  • arg 1:
    • 'query' = num conserved / length of query seq (without gaps)
    • 'hit' = num conserved / length of hit seq (without gaps)
    • 'total' = num conserved / length of alignment (with gaps)
    • default = 'total'
  • arg 2: [optional] frac conserved value to set for the type requested

🌈 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

🎀 percent_identity

• Title — percent_identity
• Usage — my $percentid = $hsp->percent_identity()
• Function — Returns the calculated percent identity for an HSP
• Returns — floating point between 0 and 100
• Args — none

🌸 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)

🙈 yes this is a whole vibe check on your frame math. GFF says 0-2, BLAST says 1-3, and negative frames? deduced by peeking at the strand. iykyk.

🦋 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

💀 not me pointing out that the Usage literally says gel_aln and not get_aln. keeping it exactly as the ancestors wrote it, no cap.

💅 num_conserved

• Title — num_conserved
• Usage — $obj->num_conserved($newval)
• Function — returns the number of conserved residues in the alignment
• Returns — inetger (yes bestie, the original really says inetger, we stan a typo 👑)
• Args — integer (optional)

✨ num_identical

• Title — num_identical
• Usage — $obj->num_identical($newval)
• Function — returns the number of identical residues in the alignment
• Returns — integer
• Args — integer (optional)

🔥 seq_inds

• Title — seq_inds
• Purpose — Get a list of residue positions (indices) for all identical or conserved residues in the query or sbjct sequence.
• Example —

@s_ind = $hsp->seq_inds('query', 'identical');
@h_ind = $hsp->seq_inds('hit', 'conserved');
@h_ind = $hsp->seq_inds('hit', 'conserved', 1);

• Returns — List of integers. May include ranges if collapse is true.
• Argument —
  • seq_type = 'query' or 'hit' or 'sbjct' (default = query)
    • ('sbjct' is synonymous with 'hit')
  • class = 'identical' or 'conserved' or 'nomatch' or 'gap' (default = identical) (can be shortened to 'id' or 'cons')
  • collapse = boolean, if true, consecutive positions are merged using a range notation, e.g., "1 2 3 4 5 7 9 10 11" collapses to "1-5 7 9-11". This is useful for consolidating long lists. Default = no collapse.
• Throws — n/a.
• Comments — (nothing here, she's mysterious 🌙)

See Also — Bio::Search::BlastUtils::collapse_nums(), Bio::Search::Hit::HitI::seq_inds()

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💜 Inherited from Bio::SeqFeature::SimilarityPair 💜

These methods come from Bio::SeqFeature::SimilarityPair, and they're all yours for free, bestie. periodt.

🌈 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

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and that's the whole page, bestie, you ate it 🍽️✨ this absolute icon of a manual page is perl v5.30.0, dated 2019-10-29, and it lives under the name Bio::S...MERHSP(3pm). go forth and parse your HSPs, main character 💅👑