# BioPerl module for Bio::Tools::Run::Phylo::Phylip::SeqBoot
#
# Created by
#
# Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Phylo::Phylip::SeqBoot - Wrapper for the phylip
program SeqBoot
=head1 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);
}
=head1 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.
=head1 PARAMETERS FOR SEQBOOT
=head2 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
=head2 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
=head2 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
=head2 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
=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 $ENV{PHYLIPDIR};
}
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/PROGRAM/i) {
$self->executable($value);
next;
}
if ($attr =~ /IDLENGTH/i){
$self->idlength($value);
next;
}
$self->$attr($value);
}
return $self;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 idlength
Title : idlength
Usage : $obj->idlength ($newval)
Function:
Returns : value of idlength
Args : newvalue (optional)
=cut
sub idlength{
my $self = shift;
if( @_ ) {
my $value = shift;
$self->{'idlength'} = $value;
}
return $self->{'idlength'};
}
=head2 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.
=cut
sub run{
my ($self,$input) = @_;
my ($infilename);
# Create input file pointer
$infilename = $self->_setinput($input);
if (!$infilename) {$self->throw("Problems setting up for seqboot. Probably bad input data in $input !");}
# Create parameter string to pass to SeqBoot program
my $param_string = $self->_setparams();
# run SeqBoot
my $aln = $self->_run($infilename,$param_string);
return $aln;
}
#################################################
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to SeqBoot program
Example :
Returns : an array ref of <Bio::SimpleAlign>
Args : Name of a file containing a set of multiple alignments in Phylip format
and a parameter string to be passed to SeqBoot
=cut
sub _run {
my ($self,$infile,$param_string) = @_;
my $instring;
my $curpath = cwd;
unless( File::Spec->file_name_is_absolute($infile) ) {
$infile = $self->io->catfile($curpath,$infile);
}
#odd random seed
my $rand = (2 * int(rand(10000)) + 1);
if ($self->version == 3.5){
$instring = $infile."\n$rand\n$param_string";
}
else {
$instring = $infile."\n$param_string$rand\n";
}
$self->debug( "Program ".$self->executable." $instring\n");
chdir($self->tempdir);
#open a pipe to run SeqBoot to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) {
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
open(SeqBoot,"|".$self->executable .">$null");
}
else {
open(SeqBoot,"|".$self->executable);
}
print SeqBoot $instring;
close(SeqBoot);
# get the results
my $outfile = $self->io->catfile($self->tempdir,$self->outfile);
chdir($curpath);
$self->throw("SeqBoot did not create files correctly ($outfile)")
unless (-e $outfile);
#parse the alignments
my @aln;
my @parse_params;
push @parse_params, ('-interleaved' => 1) if $self->version == 3.6;
my $aio = Bio::AlignIO->new(-file=>$outfile,-format=>"phylip",
@parse_params);
while (my $aln = $aio->next_aln){
push @aln, $aln;
}
# Clean up the temporary files created along the way...
unlink $outfile unless $self->save_tempfiles;
return \@aln;
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for SeqBoot program
Example :
Returns : name of file containing a multiple alignment in Phylip format
Args : SimpleAlign object reference or input file name
=cut
sub _setinput {
my ($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
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
=cut
=head2 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
=cut
=head2 cleanup
Title : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory after a SeqBoot run
Returns : none
Args : none
=cut
=head2 io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
=cut
1; # Needed to keep compiler happy