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

✨ NAME ✨

Bio::Search::Hit::HMMERHit — a Hit module for HMMER hits 💖 (that's the whole vibe, bestie, it's a Bio::Search::Hit::HMMERHit(3pm) situation)

---

🌸 SYNOPSIS 🌸

use Bio::Search::Hit::HMMERHit;
my $hit = Bio::Search::Hit::HMMERHit->new();
# use it in the same way as Bio::Search::Hit::GenericHit

---

🦋 DESCRIPTION 🦋

Okay so real talk: this is a specialization of Bio::Search::Hit::GenericHit. It brings a couple of new methods to the function — next_domain and domains — and that's the tea. ☕

Heads up though: bits and iteration make no sense for this object and will return 0. Not a bug, just the way it is. Don't come for me. 💀

---

💌 FEEDBACK 💌

🎀 Mailing Lists 🎀

User feedback is, like, literally an integral part of the evolution of this and other Bioperl modules. 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 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. (Yes, code and data examples — help them help you, periodt. 💅)

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

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

---

👑 AUTHOR - Jason Stajich 👑

Email jason@bioperl.org — icon behavior, honestly. 💜

---

📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. (iykyk 🔥)

---

🌟 new 🌟

• Title: new
• Usage: my $obj = Bio::Search::Hit::HMMERHit->new();
• Function: Builds a new Bio::Search::Hit::HMMERHit object
• Returns: Bio::Search::Hit::HMMERHit
• Args: (none)

Plus the Bio::Search::Hit::GenericHit inherited params:

• -name => Name of Hit (required)
• -description => Description (optional)
• -accession => Accession number (optional)
• -length => Length of the Hit (optional)
• -score => Raw Score for the Hit (optional)
• -significance => Significance value for the Hit (optional)
• -algorithm => Algorithm used (BLASTP, FASTX, etc...)
• -hsps => Array ref of HSPs for this Hit.

---

🧚 next_domain 🧚

• Title: next_domain
• Usage: my $domain = $hit->next_domain();
• Function: An alias for L<next_hsp()>, this will return the next HSP
• Returns: L<Bio::Search::HSP::HSPI> object
• Args: none

---

🍓 domains 🍓

• Title: domains
• Usage: my @domains = $hit->domains();
• Function: An alias for L<hsps()>, this will return the full list of hsps
• Returns: array of L<Bio::Search::HSP::HSPI> objects
• Args: none

---

💫 inherited Bio::Search::Hit::GenericHit methods 💫

⭐ add_hsp ⭐

• Title: add_hsp
• Usage: $hit->add_hsp($hsp)
• Function: Add a HSP to the collection of HSPs for a Hit
• Returns: number of HSPs in the Hit
• Args: Bio::Search::HSP::HSPI object

---

💖 Bio::Search::Hit::HitI methods 💖

🌸 name 🌸

• Title: name
• Usage: $hit_name = $hit->name();
• Function: returns the name of the Hit sequence
• Returns: a scalar string
• Args: [optional] scalar string to set the name

🎀 accession 🎀

• Title: accession
• Usage: $acc = $hit->accession();
• Function: Retrieve the accession (if available) for the hit
• Returns: a scalar string (empty string if not set)
• Args: none

🦋 description 🦋

• Title: description
• Usage: $desc = $hit->description();
• Function: Retrieve the description for the hit
• Returns: a scalar string
• Args: [optional] scalar string to set the description

✨ length ✨

• Title: length
• Usage: my $len = $hit->length
• Function: Returns the length of the hit
• Returns: integer
• Args: [optional] integer to set the length

🔥 algorithm 🔥

• Title: algorithm
• Usage: $alg = $hit->algorithm();
• Function: Gets the algorithm specification that was used to obtain the hit. For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna).
• Returns: a scalar string
• Args: [optional] scalar string to set the algorithm

💅 raw_score 💅

• Title: raw_score
• Usage: $score = $hit->raw_score();
• Function: Gets the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable.
• Returns: a scalar value
• Args: [optional] scalar value to set the raw score

🌈 significance 🌈

• Title: significance
• Usage: $significance = $hit->significance();
• Function: Used to obtain the E or P value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef.
• Returns: a scalar value or undef if unavailable
• Args: [optional] scalar value to set the significance

💀 bits 💀

• Usage: $hit_object->bits();
• Purpose: Gets the bit score of the best HSP for the current hit.
• Example: $bits = $hit_object->bits();
• Returns: Integer or undef if bit score is not set
• Argument: n/a

See Also: score()

Reminder bestie: for this object, bits makes no sense and returns 0. 🙈

🧚 next_hsp 🧚

• Title: next_hsp
• Usage: while( $hsp = $obj->next_hsp()) { ... }
• Function: Returns the next available High Scoring Pair
• Example: (none given)
• Returns: Bio::Search::HSP::HSPI object or null if finished
• Args: none

⭐ hsps ⭐

• Usage: $hit_object->hsps();
• Purpose: Get a list containing all HSP objects. : Get the numbers of HSPs for the current hit.
• Example: @hsps = $hit_object->hsps(); : $num = $hit_object->hsps(); # alternatively, use num_hsps()
• Returns: Array context : list of Bio::Search::HSP::BlastHSP.pm objects. : Scalar context: integer (number of HSPs). : (Equivalent to num_hsps()).
• Argument: n/a. Relies on wantarray
• Throws: Exception if the HSPs have not been collected.

See Also: hsp(), num_hsps()

🍓 num_hsps 🍓

• Usage: $hit_object->num_hsps();
• Purpose: Get the number of HSPs for the present Blast hit.
• Example: $nhsps = $hit_object->num_hsps();
• Returns: Integer
• Argument: n/a
• Throws: Exception if the HSPs have not been collected.

See Also: hsps()

🎀 rewind 🎀

• Title: rewind
• Usage: $hit->rewind;
• Function: Allow one to reset the HSP iteration to the beginning. Since this is an in-memory implementation
• Returns: none
• Args: none

🌟 iteration 🌟

• Title: iteration
• Usage: $obj->iteration($newval)
• Function: PSI-BLAST iteration
• Returns: value of iteration
• Args: newvalue (optional)

And yeah — for this object iteration makes no sense either and returns 0. 😭

---

That's the whole page, bestie, no notes. 🫶 This was perl v5.30.0, dated 2019-10-29, and it's giving absolute classic Bioperl energy — go forth and annotate your HMMER hits. 💜✨