Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

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://bugzilla.open-bio.org/
 
 

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