view release on metacpan or  search on metacpan

lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm  view on Meta::CPAN

            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 

=head1 FEEDBACK

=head2 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

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 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/

=head1 AUTHOR - Shawn Hoon 

Email shawnh@fugu-sg.org 

=head1 APPENDIX

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

=cut

#'

	
package Bio::Tools::Run::Phylo::Phylip::SeqBoot;

use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
	    @SEQBOOT_PARAMS @OTHER_SWITCHES
	    %OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Tools::Run::Phylo::Phylip::Base;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);
use Bio::Matrix::PhylipDist;
use Cwd;


# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);

# You will need to enable the SeqBoot program. This
# can be done in (at least) 3 ways:
#
# 1. define an environmental variable PHYLIPDIR:
# export PHYLIPDIR=/home/shawnh/PHYLIP/bin
#
# 2. include a definition of an environmental variable CLUSTALDIR in
# every script that will use Clustal.pm.
# $ENV{PHYLIPDIR} = '/home/shawnh/PHYLIP/bin';
#
# 3. You can set the path to the program through doing:
# my @params('executable'=>'/usr/local/bin/seqboot');
# my $SeqBoot_factory = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params);
# 


BEGIN {
	@SEQBOOT_PARAMS = qw(DATATYPE PERMUTE BLOCKSIZE REPLICATES READWEIGHTS READCAT);
	@OTHER_SWITCHES = qw(QUIET);
	foreach my $attr(@SEQBOOT_PARAMS,@OTHER_SWITCHES) {
		$OK_FIELD{$attr}++;
	}
}

=head2 program_name

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

=cut

sub program_name {
  return 'seqboot';
}

=head2 program_dir

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

=cut

sub program_dir {
  return Bio::Root::IO->catfile($ENV{PHYLIPDIR}) if $ENV{PHYLIPDIR};
}

lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm  view on Meta::CPAN

=head2  _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


=cut

sub _setinput {
    my ($self, $input) = @_;
    my ($alnfilename,$tfh);
  
    #  a phy formatted alignment file 
  	unless (ref $input) {
        # check that file exists or throw
        $alnfilename= $input;
        unless (-e $input) {return 0;}
		   return $alnfilename;
    }
    my @input = ref($input) eq 'ARRAY' ? @{$input}: ($input);

    ($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir);
    my $alnIO = Bio::AlignIO->new(-fh => $tfh, 
	                      			      -format=>'phylip',
                      				      -idlength=>$self->idlength());
    foreach my $input(@input){
    #  $input should be a Bio::Align::AlignI 
      $input->isa("Bio::Align::AlignI") || $self->throw("Expecting a Bio::Align::AlignI object");
      #  Open temporary file for both reading & writing of BioSeq array
    	$alnIO->write_aln($input);
    }
    $alnIO->close();
    close($tfh);
    return $alnfilename;		
}

=head2  _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

=cut

sub _setparams {
    my ($attr, $value, $self);

    #do nothing for now
    $self = shift;
    my $param_string = "";
    my $cat = 0;
    my $gene_freq = 0;
    my %menu = %{$Menu{$self->version}->{'SEQBOOT'}};

    foreach  my $attr ( @SEQBOOT_PARAMS) {
    	$value = $self->$attr();
    	next unless (defined $value);
    	if ($attr =~/REPLICATES/i){
        if( $value !~ /(\d+(\.\d+)?)/ ) {
            $self->warn("Expected a number in  $attr\n");
            next;
        }
		   $param_string .= $menu{'REPLICATES'}."$value\n";
      }
      elsif($attr=~/DATATYPE/i){
          $gene_freq = 1 if $value =~/GENEFREQ/i;
          $param_string .= $menu{'DATATYPE'}{uc $value};
      }
      else {
       if($attr =~/ALLELES/i){
           if(!$gene_freq){
             $self->warn("Alleles options only be used with alleles option");
             return;
           }
           $param_string .=$menu{uc $attr};
       }
      }
	  }
    $param_string .= $menu{'SUBMIT'};

    return $param_string;
}



=head1 Bio::Tools::Run::Wrapper methods

=cut

=head2 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)


=cut

=head2 save_tempfiles

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


=cut

=head2 outfile_name