Bio::T...:Domain(3pm)

💖 NAME 💖

Bio::Tools::HMMER::Domain — one particular domain hit from HMMER. Like, one domain. Singular. A whole little guy. 🎀

This is a page from the User Contributed Perl Documentation, bestie, so pull up a chair.

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✨ SYNOPSIS ✨

Read the Bio::Tools::HMMER::Results docs. That's it. That's the synopsis. The original really said "go read the other page" and honestly? Respect. 💅

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🌸 DESCRIPTION 🌸

Okay so. This thing is a particular domain score. That's its whole deal.

We reuse the Homol SeqFeature system here, so this object inherits off Homol SeqFeature. And because this code originally came from a separate project, there's some backward-compatibility stuff hanging around to keep old code working. Not our fault, we just live here. 🙈

And don't forget — it also inherits off Bio::SeqFeature, so all your usual nice start/end/score stuff is ready for use. It's giving "I contain multitudes". 🔥

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📬 CONTACT 📬

Ewan Birney, birney@ebi.ac.uk

🫶 CONTRIBUTORS 🫶

Jason Stajich, jason@bioperl.org

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🔍 APPENDIX 🔍

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — that's the tell, iykyk. 👑

🦋 add_alignment_line

• Title: add_alignment_line
• Usage: $domain->add_alignment_line($line_from_hmmer_output);
• Function: add an alignment line to this Domain object
• Returns: Nothing
• Args: scalar

Adds an alignment line. Mostly this is here so we can store the HMMER alignments as flat text that can be regurgitated later. And yeah — you're right. This is not nice and not the right way to do it. C'est la vie. 💀

🦋 each_alignment_line

• Title: each_alignment_line
• Usage: foreach $line ( $domain->each_alignment_line )
• Function: regurgitates the alignment lines as they were fed in. only useful realistically for printing.
• Example: —
• Returns: —
• Args: None

🦋 get_nse

• Title: get_nse
• Usage: $domain->get_nse()
• Function: Provides a seqname/start-end format, useful for unique keys. nse stands for name-start-end. It is used a lot in Pfam.
• Example: —
• Returns: A string
• Args: Optional separator 1 and separator 2 (default / and -)

Two separators, both optional, both with defaults. She's flexible. 💅

🦋 hmmacc

• Title: hmmacc
• Usage: $domain->hmmacc($newacc)
• Function: set get for HMM accession number. This is placed in the homol feature of the HMM
• Example: —
• Returns: —
• Args: —

🦋 hmmname

• Title: hmmname
• Usage: $domain->hmmname($newname)
• Function: set get for HMM accession number. This is placed in the homol feature of the HMM
• Example: —
• Returns: —
• Args: —

Yes, hmmname's Function line says "accession number" too. We are faithfully reporting what the original says. Not a typo we invented, bestie, we just work here. 🌸

🦋 bits

• Title: bits
• Usage: —
• Function: backward compatibility. Same as score
• Example: —
• Returns: —
• Args: —

🦋 evalue

• Title: evalue
• Usage: —
• Function: $domain->evalue($value);
• Example: —
• Returns: —
• Args: —

🦋 seqbits

• Title: seqbits
• Usage: —
• Function: $domain->seqbits($value);
• Example: —
• Returns: —
• Args: —

🦋 seq_range

• Title: seq_range
• Usage: —
• Function: Throws an exception to catch scripts which need to upgrade
• Example: —
• Returns: —
• Args: —

🦋 hmm_range

• Title: hmm_range
• Usage: —
• Function: Throws an exception to catch scripts which need to upgrade
• Example: —
• Returns: —
• Args: —

⚠️ Both seq_range and hmm_range are deliberately explosive — they exist to throw so your old script gets caught and you go upgrade it. That's the point. Don't come crying to me when it yells at you. 😭

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perl v5.30.0 · 2019-10-29

And that's the whole page, bestie — this one's from perl v5.30.0, dated 2019-10-29, and it ate, no notes. Go read Bio::Tools::HMMER::Results like the synopsis told you to. 💖✨🦋