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 : DATATYPEDescription : (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 : ALLELESDescription : (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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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 web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Shawn Hoon
Email [email protected]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