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

	 #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}){

	 # 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(
		    -format=>"fasta");		     #	FASTA output to	view full names
	 foreach my $ai(@{$aln_ref}){
		my $new_aln=$ai->restore_displayname($ref_name); #  Restore names

       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.

       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

       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

		    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

	 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

       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

   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.			- General discussion	- About	the mailing lists

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

       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

AUTHOR - Shawn Hoon

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

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

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

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

	Title	: run
	Usage	:
	       $inputfilename =	't/data/prot.phy';
	       $matrix=	$seqboot_factory->run($inputfilename);
	       $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.

	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

	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

	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
	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)

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

	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

	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

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

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

perl v5.32.1			  20Bio::Tools::Run::Phylo::Phylip::SeqBoot(3)


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