Bio::Tools::Run::Hmmer.3pm

Langue: en

Version: 2005-04-27 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

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();
 
   my $factory =  Bio::Tools::Run::Hmmer->new('program'=>'hmmalign',
                                              'hmm'=>'model.hmm');
 
    # Pass the factory a Bio::Seq object or a file name
 
    # returns a Bio::AlignIO object
    my $aio = $factory->run($seq);
 
 

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 the web:

  http://bugzilla.bioperl.org/
 
 

AUTHOR - Shawn Hoon

  Email: shawnh-at-gmx.net
 
 

CONTRIBUTORS

  Shawn Hoon shawnh-at-gmx.net
  Jason Stajich jason -at- bioperl -dot- org
  Scott Markel scott -at- scitegic -dot com
 
 

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    :