NAME

Bio::Tools::Run::Phylo::Phylip::SeqBoot - Wrapper for the phylip program SeqBoot

SYNOPSIS

  #Create a SimpleAlign object
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  $inputfilename = 't/data/cysprot.fa';
  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.

  # Use seqboot to generate bootstap alignments
  my @params = ('datatype'=>'SEQUENCE','replicates'=>100);
  my $seq = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params);

  my $aln_ref = $seq->run($aln);

  my $aio = Bio::AlignIO->new(-file=>">alignment.bootstrap",-format=>"phylip");
  foreach my $ai(@{$aln_ref}){
         $aio->write_aln($ai);
  }

  # To prevent PHYLIP from truncating sequence names:
  # Step 1. Shelf the original names:
  my ($aln_safe, $ref_name)=                  #  $aln_safe has serial names
             $aln->set_displayname_safe();    #  $ref_name holds orginal names 
  # Step 2. Run PHYLIP programs:
  $aln_ref = $seq->run($aln_safe);            #  Use $aln_safe instead of $aln
  # Step 3. Retrieve orgininal names
  $aio = Bio::AlignIO->new(
             -file=>">alignment.bootstrap",
             -format=>"fasta");               #  FASTA output to view full names
  foreach my $ai(@{$aln_ref}){
         my $new_aln=$ai->restore_displayname($ref_name); #  Restore names
         $aio->write_aln($new_aln);
  }

DESCRIPTION

Wrapper for seqboot from the phylip package by Joseph Felsentein.

Taken from phylip doc...

"SEQBOOT is a general boostrapping tool. It is intended to allow you to generate multiple data sets that are resampled versions of the input data set. SEQBOOT can handle molecular sequences, binary characters, restriction sites, or gene frequencies."

More documentation on using seqboot and setting parameters may be found in the phylip package.

VERSION Support This wrapper currently supports v3.5 of phylip. There is also support for v3.6 although this is still experimental as v3.6 is still under alpha release and not all functionalities maybe supported.

PARAMETERS FOR SEQBOOT

MODEL

Title : DATATYPE Description : (optional)

                  This program supports 3 different datatypes
                  SEQUENCE: Molecular Sequences
                  MORPH   : Discrete  Morphological  Characters
                  REST    : Restriction Sites
                  GENEFREQ: Gene  Frequencies

             Defaults to SEQUENCE

PERMUTE

Title: PERMUTE Description: (optional)

             3 different resampling methods are available:

             BOOTSTRAP : creating a new data set by sampling N
                         characters randomly with replacement The
                         resulting data set has the same size as the
                         original, but some characters have been left
                         out and others are duplicated

             JACKKNIFE : Delete-half-jackknifing. It involves sampling
                         a random half of the characters, and
                         including them in the data but dropping the
                         others The resulting data sets are half the
                         size of the original, and no characters are
                         duplicated.

             PERMUTE : Permuting species within characters. It
                       involves permuting the columns of the data
                       matrix separately.  This produces data matrices
                       that have the same number and kinds of
                       characters but no taxonomic structure.

             Defaults to BOOTSTRAP

REPLICATES

  Title         : REPLICATES
  Description   : (optional)

                This options allows the user to set the number of
                replicate data sets. Most statisticians would be
                happiest with 1000 to 10,000 replicates in a
                bootstrap, but 100 gives a good rough picture

                Defaults to 100

ALLELES

Title : ALLELES Description : (optional)

            This option is to be used with gene frequencies datatype
            option to specify that all alleles at each locus are in
            the input file.

                  Defaults to NULL

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://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. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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

AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.org

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   : >program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

program_dir

 Title   : program_dir
 Usage   : ->program_dir()
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :

idlength

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

run

 Title   : run 
 Usage   :
        $inputfilename = 't/data/prot.phy';
        $matrix= $seqboot_factory->run($inputfilename);
or
        $seq_array_ref = \@seq_array; @seq_array is array of Seq objs
        $aln = $clustalw_factory->align($seq_array_ref);
        $aln_ref = $SeqBootfactory->run($aln);

 Function: Create bootstrap sets of alignments
 Example :
 Returns : an array ref of L<Bio::SimpleAlign>
 Args    : Name of a file containing a multiple alignment in Phylip format
           or an SimpleAlign object 

 Throws an exception if argument is not either a string (eg a
 filename) or a Bio::SimpleAlign object. If
 argument is string, throws exception if file corresponding to string
 name can not be found.

_run

 Title   :  _run
 Usage   :  Internal function, not to be called directly        
 Function:  makes actual system call to SeqBoot program
 Example :
 Returns : an array ref of <Bio::SimpleAlign> 
 Args    : Name of a file containing a set of multiple alignments in Phylip format 
           and a parameter string to be passed to SeqBoot

_setinput()

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly        
 Function:   Create input file for SeqBoot program
 Example :
 Returns : name of file containing a multiple alignment in Phylip format 
 Args    : SimpleAlign object reference or input file name

_setparams()

 Title   :  _setparams
 Usage   :  Internal function, not to be called directly        
 Function:   Create parameter inputs for SeqBoot program
 Example :
 Returns : parameter string to be passed to SeqBoot
 Args    : name of calling object

Bio::Tools::Run::Wrapper methods

no_param_checks

 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values  
 Returns : value of no_param_checks
 Args    : newvalue (optional)

save_tempfiles

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

outfile_name

 Title   : outfile_name
 Usage   : my $outfile = $SeqBoot->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to

tempdir

 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none

cleanup

 Title   : cleanup
 Usage   : $codeml->cleanup();
 Function: Will cleanup the tempdir directory after a SeqBoot run
 Returns : none
 Args    : none

io

 Title   : io
 Usage   : $obj->io($newval)
 Function:  Gets a L<Bio::Root::IO> object
 Returns : L<Bio::Root::IO>
 Args    : none