/ 
bioperl-run-1.4
/ Bio::Tools::Run::Hmmer

NAME

Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmsearch ,hmmbuild, hmmcalibrate, hmmalign, hmmpfam

SYNOPSIS

#run hmmpfam|hmmalign|hmmsearch
my $factory = Bio::Tools::Run::Hmmer->new('program'=>'hmmsearch','hmm'=>'model.hmm');

# Pass the factory a Bio::Seq object or a file name

# returns a Bio::SearchIO object
my $search = $factory->run($seq);


my @feat;
while (my $result = $searchio->next_result){
 while(my $hit = $result->next_hit){
  while (my $hsp = $hit->next_hsp){
          print join("\t", ( $r->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 using hmmbuild
my $aio = Bio::AlignIO->new(-file=>"protein.msf",-format=>'msf');
my $aln = $aio->next_aln;
my $factory =  Bio::Tools::Run::Hmmer->new('program'=>'hmmbuild','hmm'=>'model.hmm');
$factory->run($aln);

#calibrate the hmm
my $factory =  Bio::Tools::Run::Hmmer->new('program'=>'hmmcalibrate','hmm'=>'model.hmm');
$factory->run();

DESCRIPTION

Wrapper module for Sean Eddy's HMMER suite of program to allow running of hmmsearch,hmmpfam,hmmalign, hmmbuild,hmmconvert. Binaries are available at http://hmmer.wustl.edu/

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. 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://bio.perl.org/MailList.html             - About the mailing lists

Reporting Bugs

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

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Shawn

Email: shawnh@gmx.net

CONTRIBUTORS

Shawn Hoon shawnh@gmx.net

APPENDIX

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

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, obtiained from ENV variable.
Returns:  string
Args    :

new

Title   : new
Usage   : $HMMER->new(@params)
Function: creates a new HMMER factory
Returns:  Bio::Tools::Run::HMMER
Args    :

run

Title   :   run
Usage   :   $obj->run($seqFile)
Function:   Runs HMMER and returns Bio::SearchIO
Returns :   A Bio::SearchIO
Args    :   A Bio::PrimarySeqI or file name

_run

Title   :   _run
Usage   :   $obj->_run()
Function:   Internal(not to be used directly)
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :

_setparams

Title   :  _setparams
Usage   :  Internal function, not to be called directly
Function:  creates a string of params to be used in the command string
Example :
Returns :  string of params
Args    :

_writeSeqFile

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

_writeAlignFile

Title   :   _writeAlignFile
Usage   :   obj->_writeAlignFile($seq)
Function:   Internal(not to be used directly)
Returns :
Args    :