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

💖 Bio::Tools::Run::Hmmer 💖

okay so bestie, welcome to Bio::Tools::Run::Hmmer — this is the Perl module (a 3pm page, if you're keeping track) that wraps up local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, and hmmsearch. she's giving wrapper-for-Sean-Eddy's-HMMER-suite energy and honestly? iconic.

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✨ NAME ✨

Bio::Tools::Run::Hmmer — a wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch. six programs, one little module, no cap.

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🌸 SYNOPSIS 🌸

run hmmsearch (and it's the same deal for hmmpfam, just so you know):

# run hmmsearch (similar for hmmpfam)
my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm');

# Pass the factory a Bio::Seq object or a file name, returns a Bio::SearchIO
my $searchio = $factory->hmmsearch($seq);

while (my $result = $searchio->next_result){
 while(my $hit = $result->next_hit){
  while (my $hsp = $hit->next_hsp){
          print join("\t", ( $result->query_name,
                             $hsp->query->start,
                             $hsp->query->end,
                             $hit->name,
                             $hsp->hit->start,
                             $hsp->hit->end,
                             $hsp->score,
                             $hsp->evalue,
                             $hsp->seq_str,
                             )), "\n";
  }
 }
}

build a hmm with hmmbuild:

# build a hmm using hmmbuild
my $aio = Bio::AlignIO->new(-file => "protein.msf", -format => 'msf');
my $aln = $aio->next_aln;
my $factory =  Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm');
$factory->hmmbuild($aln);

calibrate that hmm:

# calibrate the hmm
$factory->calibrate();

emit a sequence stream from the hmm:

# emit a sequence stream from the hmm
my $seqio = $factory->hmmemit();

and align sequences to the hmm:

# align sequences to the hmm
my $alnio = $factory->hmmalign(@seqs);

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🦋 DESCRIPTION 🦋

so this is a wrapper module for Sean Eddy's HMMER suite of programs, and it exists so you can run hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam and hmmsearch from Perl without losing your mind. the binaries are available at http://hmmer.janelia.org/ — go get 'em.

you can pass most of the options that the command-line programs understand straight into new(), OR you can set those options later by calling methods with the same name as the argument. either way works! and in both instances, case sensitivity matters. like, it matters matters. 💅

there's also an extra method, hmm(), to specify the hmm file (which every single HMMER program needs, jsyk) — you'd normally just set that in your call to new().

🚨 the HMMER programs must EITHER be in your path, OR you must set the environment variable HMMERDIR to point to their location. no third option, bestie, that's the vibe check.

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — genuinely, they want to hear from you. send your comments and suggestions preferably to one of the Bioperl mailing lists. 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. the reason is lowkey wholesome: many experienced and reponsive experts will be able look at the problem and quickly address it. if at all possible, please include a thorough description of the problem with code and data examples. receipts help everyone. 🙏

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system — it helps them keep track of the bugs and their resolution. bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHOR - Shawn Hoon 👑

Email: shawnh-at-gmx.net

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🌈 CONTRIBUTORS 🌈

Shawn Hoon shawnh-at-gmx.net
Jason Stajich jason -at- bioperl -dot- org
Scott Markel scott -at- scitegic -dot com
Sendu Bala bix@sendu.me.uk

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⭐ APPENDIX ⭐

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (that underscore is the "do not touch, bestie" marker).

🧚 new

Title   : new
Usage   : $HMMER->new(@params)
Function: Creates a new HMMER factory
Returns : Bio::Tools::Run::HMMER
Args    : -hmm => filename # the hmm, used by all program types; if not set
                           # here, must be set with hmm() method prior to
                           # running anything
          -_READMETHOD => 'hmmer' (default) || 'hmmer_pull' # the parsing
                                                            # module to use for
                                                            # hmmpfam/hmmsearch

          Any option supported by a Hmmer program, where switches are given
          a true value, eg. -q => 1, EXCEPT for the following which are handled
          internally/ incompatible: h verbose a compat pvm

          WARNING: the default sequence format passed to hmmpfam is msf. If
          you are using a different format, you need to pass it with informat.
          e.g.
          my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm',
                                                    -informat => 'fasta');

          -q is synonymous with -quiet
          -o is synonymous with -outfile

          # may be specified here, allowing run() to be used, or
          # it can be omitted and the corresponding method (eg.
          # hmmalign()) used later.
          -program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch

⚠️ real talk: the default sequence format passed to hmmpfam is msf. if you're using a different format you need to pass it with informat, okay? don't come crying to me when it doesn't parse. also, the options h verbose a compat pvm are handled internally or are incompatible — so don't pass those.

🔥 run

Title   : run
Usage   : $obj->run($seqFile)
Function: Runs one of the Hmmer programs, according to the current setting of
          program() (as typically set during new(-program => 'name')).
Returns : A Bio::SearchIO, Bio::AlignIO, Bio::SeqIO or boolean depending on
          the program being run (see method corresponding to program name for
          details).
Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename

💜 hmmalign

Title   : hmmalign
Usage   : $obj->hmmalign()
Function: Runs hmmalign
Returns : A Bio::AlignIO
Args    : list of Bio::SeqI OR Bio::Align::AlignI OR filename of file with
          sequences or an alignment

🌸 hmmbuild

Title   : hmmbuild
Usage   : $obj->hmmbuild()
Function: Runs hmmbuild, outputting an hmm to the file currently set by method
          hmm() or db(), or failing that, o() or outfile(), or failing that, to
          a temp location.
Returns : true on success
Args    : Bio::Align::AlignI OR filename of file with an alignment

✨ hmmcalibrate

Title   : hmmcalibrate
Usage   : $obj->hmmcalibrate()
Function: Runs hmmcalibrate
Returns : true on success
Args    : none (hmm() must be set, most likely by the -hmm option of new()), OR
          optionally supply an hmm filename to set hmm() and run

🦋 hmmemit

Title   : hmmemit
Usage   : $obj->hmmemit()
Function: Runs hmmemit
Returns : A Bio::SeqIO
Args    : none (hmm() must be set, most likely by the -hmm option of new()), OR
          optionally supply an hmm filename to set hmm() and run

💖 hmmpfam

Title   : hmmpfam
Usage   : $obj->hmmpfam()
Function: Runs hmmpfam
Returns : A Bio::SearchIO
Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename

🎀 hmmsearch

Title   : hmmsearch
Usage   : $obj->hmmsearch()
Function: Runs hmmsearch
Returns : A Bio::SearchIO
Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename

🧚 _setinput

Title   : _setinput
Usage   : $obj->_setinput()
Function: Internal(not to be used directly)
Returns : filename
Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename

💅 _run

Title   : _run
Usage   : $obj->_run()
Function: Internal(not to be used directly)
Returns : Bio::SearchIO
Args    : file name

⭐ _setparams

Title   : _setparams
Usage   : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Returns : string of params
Args    : none

🌈 program_name

Title   : program_name
Usage   : $factory>program_name()
Function: holds the program name
Returns : string
Args    : none

🔥 program_dir

Title   : program_dir
Usage   : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args    : none

🍓 _writeSeqFile

Title   : _writeSeqFile
Usage   : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : filename
Args    : list of Bio::SeqI

👑 _writeAlignFile

Title   : _writeAlignFile
Usage   : obj->_writeAlignFile($seq)
Function: Internal(not to be used directly)
Returns : filename
Args    : list of Bio::Align::AlignI

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and that's the whole page, bestie!! 🫶✨ this one's from perl v5.36.0, dated 2023-01-22, and it lives under the name Bio::T...:Hmmer(3pm) in the User Contributed Perl Documentation. go forth and align ur sequences. mwah 💋