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

💖 Bio::Tools::HMMER::Results 💖

okay so bestie, welcome to Bio::T...esults(3pm) — that's the man page for Bio::Tools::HMMER::Results, straight outta the User Contributed Perl Documentation. this is the object that holds your HMMER output and it's lowkey iconic. let's get into it 🫶

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✨ NAME ✨

Bio::Tools::HMMER::Results — the object that represents HMMER output results. periodt. 💅

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🌸 SYNOPSIS 🌸

# parse a hmmsearch file (can also parse a hmmpfam file)
$res = Bio::Tools::HMMER::Results->new( -file => 'output.hmm' ,
                                       -type => 'hmmsearch');

# print out the results for each sequence
foreach $seq ( $res->each_Set ) {
    print "Sequence bit score is",$seq->bits,"\n";
    foreach $domain ( $seq->each_Domain ) {
        print " Domain start ",$domain->start," end ",$domain->end,
        " score ",$domain->bits,"\n";
    }
}

# new result object on a sequence/domain cutoff of
# 25 bits sequence, 15 bits domain
$newresult = $res->filter_on_cutoff(25,15);

# alternative way of getting out all domains directly
foreach $domain ( $res->each_Domain ) {
    print "Domain on ",$domain->seq_id," with score ",
    $domain->bits," evalue ",$domain->evalue,"\n";
}

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🦋 DESCRIPTION 🦋

so this object is literally your HMMER output, whether it came from hmmsearch or hmmpfam. for hmmsearch, you get a whole series of HMMER::Set objects, one for each sequence, and each one has the bits score for the object. for hmmpfam searches? only one Set object gets made. that's it, that's the vibe.

now for the lore 👑 — these objects come from the original HMMResults modules that were used internally in Pfam, written by Ewan Birney. Ewan then converted them into BioPerl objects back in 1999. that conversion is meant to be backwardly compatible, but it might not be. caveat emptor, bestie. 💀

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📬 FEEDBACK 📬

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. send your comments and suggestions preferably to one of the Bioperl mailing lists — 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

and not to the module maintainer directly, okay? there are so many experienced and responsive experts who can look at the problem and quickly address it. also pls include a thorough description of the problem with code and data examples if at all possible. we're begging 🙏

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we 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 - Ewan Birney 👑

Email birney@ebi.ac.uk

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🌈 CONTRIBUTORS 🌈

Jason Stajich, jason-at-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 _ (iykyk 👀)

🎀 next_feature

• Title: next_feature
• Usage: while( my $feat = $res->next_feature ) { # do something }
• Function: the SeqAnalysisParserI implementing function
• Example:
• Returns: a Bio::SeqFeatureI compliant object — in this case, each DomainUnit object, aka flattening the Sequence aspect of this.
• Args: None

🎀 number

• Title: number
• Usage: print "There are ",$res->number," domains hit\n";
• Function: gives you the number of domains in the HMMER report

🎀 seqfile

• Title: seqfile
• Usage: $obj->seqfile($newval)
• Function:
• Example:
• Returns: value of seqfile
• Args: newvalue (optional)

🎀 hmmfile

• Title: hmmfile
• Usage: $obj->hmmfile($newval)
• Function:
• Example:
• Returns: value of hmmfile
• Args: newvalue (optional)

🎀 add_Domain

• Title: add_Domain
• Usage: $res->add_Domain($unit)
• Function: adds a domain to the results array. mainly used internally.
• Args: a Bio::Tools::HMMER::Domain

🎀 each_Domain

• Title: each_Domain
• Usage: foreach $domain ( $res->each_Domain() )
• Function: array of Domain units which are held in this report
• Returns: array
• Args: none

🎀 domain_bits_cutoff_from_evalue

• Title: domain_bits_cutoff_from_evalue
• Usage: $cutoff = domain_bits_cutoff_from_evalue(0.01);
• Function: return a bits cutoff from an evalue using the scores here. somewhat interesting logic:
  • Find the two bit score which straddle the evalue
  • if( 25 is between these two points) return 25
  • else return the midpoint.

this logic tries to ensure that with large signal to noise separation one still has sensible 25 bit cutoff

• Returns:
• Args:

🎀 write_FT_output

• Title: write_FT_output
• Usage: $res->write_FT_output(\*STDOUT,'DOMAIN')
• Function: writes feature table output ala swissprot
• Returns:
• Args:

🎀 filter_on_cutoff

• Title: filter_on_cutoff
• Usage: $newresults = $results->filter_on_cutoff(25,15);
• Function: produces a new HMMER::Results module which has been trimmed at the cutoff.
• Returns: a Bio::Tools::HMMER::Results module
• Args: sequence cutoff and domain cutoff, in bits score. if you want one cutoff, simply use the same number both places 💫

🎀 write_ascii_out

• Title: write_ascii_out
• Usage: $res->write_ascii_out(\*STDOUT)
• Function: writes as seq seq_start seq_end model-acc model_start model_end model_name
• Returns:
• Args:

FIXME: Now that we have no modelacc, this is probably a bad thing. 💀

🎀 write_GDF_bits

• Title: write_GDF_bits
• Usage: $res->write_GDF_bits(25,15,\*STDOUT)
• Function: writes GDF format with a sequence,domain threshold
• Returns:
• Args:

🎀 add_Set

• Title: add_Set
• Usage: mainly internal function
• Function:
• Returns:
• Args:

🎀 each_Set

• Title: each_Set
• Usage:
• Function:
• Returns:
• Args:

🎀 get_Set

• Title: get_Set
• Usage: $set = $res->get_Set('sequence-name');
• Function: returns the Set for a particular sequence
• Returns: a HMMER::Set object
• Args: name of the sequence

🎀 _parse_hmmpfam

• Title: _parse_hmmpfam
• Usage: $res->_parse_hmmpfam($filehandle)
• Function:
• Returns:
• Args:

🎀 _parse_hmmsearch

• Title: _parse_hmmsearch
• Usage: $res->_parse_hmmsearch($filehandle)
• Function:
• Returns:
• Args:

🎀 parsetype

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

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and that's the whole page bestie, we ate and left no crumbs 🍓✨

this masterpiece was served to you by perl v5.30.0, dated 2019-10-29, and yes it's still filed under Bio::T...esults(3pm) because the title got truncated and honestly? iconic behavior. bye babe 💜🧚