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# BioPerl module for Bio::Tools::Run::Phylo::LVB
#
# Created by Daniel Barker, based on ProtPars.pm 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::LVB - Object for using the LVB program to create
an array of L<Bio::Tree> objects from a nucleotide multiple alignment
file or a nucleotide SimpleAlign object. Works with LVB version 2.1.
=head1 SYNOPSIS
use Bio::Tools::Run::Phylo::LVB;
# Create a SimpleAlign object.
# NOTE. Aligning nucleotide sequence directly, as below, makes
# sense for non-coding nucleotide sequence (e.g., structural RNA
# genes, introns, ITS). For protein-coding genes, to prevent
# Clustal intronducing frameshifts one should instead align the
# translations of the genes, then convert the multiple alignment
# to nucleotide by referring to the corresponding transcript
# sequences (e.g., using EMBOSS tranalign).
use Bio::Tools::Run::Alignment::Clustalw;
$aln_factory = Bio::Tools::Run::Alignment::Clustalw->new(quiet => 1);
$inputfilename = "/Users/daniel/nuc.fa";
$aln = $aln_factory->align($inputfilename);
# Create the tree or trees.
$tree_factory = Bio::Tools::Run::Phylo::LVB->new(quiet => 1);
@trees = $tree_factory->run($aln);
# Or one can pass in a file name containing a nucleotide multiple
# alignment in Phylip 3.6 format:
$tree_factory = Bio::Tools::Run::Phylo::LVB->new(quiet => 1);
$tree = $tree_factory->run("/Users/daniel/nuc.phy");
=head1 DESCRIPTION
Wrapper for LVB, which uses a simulated annealing heuristic search
to seek parsimonious trees from a nucleotide multiple alignment.
=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 PARAMETERS FOR LVB COMPUTATION
=head2 FORMAT
Title : FORMAT
Description : (optional)
When running LVB from a Phylip 3.6-format
multiple alignment file, this specifies
the layout of the file. It may be
"interleaved" or "sequential". FORMAT is
automatically set to "interleaved" if
running from a SimpleAlign object.
Defaults to "interleaved".
=head2 GAPS
Title : GAPS
Description : (optional)
LVB can treat gaps represented in the
multiple alignment by "-" as either
"fifthstate" or "unknown". "fifthstate"
regards "-" as equivalent to "O", which
is an unambiguous character state
distinct from all nucleotides. "unknown"
regards "-" as equivalent to "?", which
is as an ambiguous site that may contain
"A" or "C" or "G" or "T" or "O".
Defaults to "unknown".
=head2 SEED
Title : SEED
Description : (optional)
This specifies the random number seed
for LVB. SEED must be an integer in the
range 0 to 900000000 inclusive. If no
seed is specified, LVB takes a seed from
the system clock. By default, no seed is
specified.
=head2 DURATION
Title : DURATION
Description : (optional)
This specifies the duration of the
analysis, which may be "fast" or "slow".
"slow" causes LVB to perform a more
thorough and more time-consuming search
than "fast". Defaults to "slow".
=head2 BOOTSTRAPS
Title : BOOTSTRAPS
Description : (optional)
This specifies the number of bootstrap
replicates to use, which must be a
positive integer. Set bootstraps to 0 for
no bootstrapping. Defaults to 0.
=head1 AUTHOR
Daniel Barker
=head1 CONTRIBUTORS
Email jason-AT-bioperl_DOT_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::LVB;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
@LVB_PARAMS @OTHER_SWITCHES
%OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Cwd;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Root::Root;
use Bio::Tools::Run::WrapperBase;
use Bio::Root::IO;
use File::Copy;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
# You will need to enable the LVB program.
# You can set the path to the program through doing:
# my @params('executable'=>'/usr/local/bin/lvb');
# my $lvb_factory = Bio::Tools::Run::Phylo::LVB->new(@params);
#
BEGIN {
# NOTE. The order of the members of @LVB_PARAMS is vital!
@LVB_PARAMS = qw(FORMAT GAPS SEED DURATION BOOTSTRAPS);
@OTHER_SWITCHES = qw(QUIET);
foreach my $attr(@LVB_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 'lvb';
}
=head2 program_dir
Title : program_dir
Usage : ->program_dir()
Function: returns undef
Args :
=cut
sub program_dir {
return undef;
}
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
# set defaults
$self->FORMAT("interleaved");
$self->GAPS("unknown");
$self->SEED("");
$self->DURATION("slow");
$self->BOOTSTRAPS(0);
# re-set with user's values where specified
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
$self->$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 run
Title : run
Usage :
$inputfilename = '/Users/daniel/nuc.phy';
@trees = $factory->run($inputfilename);
Function: Create one or more LVB trees from a SimpleAlign
object or a file containing a Phylip 3.6-format
nucleotide multiple alignment.
Example :
Returns : Array of L<Bio::Tree> objects
Args : Name of a file containing a nucleotide multiple
alignment in Phylip 3.6 format, or a SimpleAlign
object
=cut
sub run{
my ($self,$input) = @_;
my ($infilename);
# Create input file pointer
$infilename = $self->_setinput($input);
if (!$infilename) {$self->throw("Problems setting up for lvb. Probably bad input data in $input !");}
# Create parameter string to pass to lvb program
my $param_string = $self->_setparams();
# run lvb
my @trees = $self->_run($infilename,$param_string);
}
=head2 create_tree
Title : create_tree
Usage :
$inputfilename = '/Users/daniel/nuc.phy';
@trees = $factory->create_tree($inputfilename);
Function: Create one or more LVB trees from a SimpleAlign
object or a file containing a Phylip 3.6-format
nucleotide multiple alignment.
Example :
Returns : Array of L<Bio::Tree> objects
Args : Name of a file containing a nucleotide multiple
alignment in Phylip 3.6 format, or a SimpleAlign
object
=cut
sub create_tree{
return shift->run(@_);
}
#################################################
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to lvb program
Example :
Returns : Array of Bio::Tree objects
Args : Name of a file containing a multiple alignment
in Phylip 3.6 format and a parameter string to be
passed to LVB
=cut
sub _run {
my ($self,$infile,$param_string) = @_;
return unless( $self->executable );
my $instring;
my $curpath = cwd;
unless( File::Spec->file_name_is_absolute($infile) ) {
$infile = $self->io->catfile($curpath,$infile);
}
$instring = $param_string;
$self->debug( "Program ".$self->executable || ''."\n");
# create LVB's working copy of the input file, which must be named "infile"
# NOTE, we cut trailing spaces since they can cause trouble with LVB 2.1
my $lvb_infile = $self->tempdir . "/infile";
open(LVB_SUB_RUN_TMP_IN_FH, "$infile");
open(LVB_SUB_RUN_TMP_OUT_FH, ">$lvb_infile");
while (<LVB_SUB_RUN_TMP_IN_FH>) {
s/ +$//;
print LVB_SUB_RUN_TMP_OUT_FH
or $self->throw("output error on $lvb_infile");
}
chdir($self->tempdir);
#open a pipe to run lvb to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) {
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
open(LVB_PIPE,"|".$self->executable.">$null");
}
else {
open(LVB_PIPE,"|".$self->executable);
}
print LVB_PIPE $instring;
close(LVB_PIPE);
chdir($curpath);
#get the results
my $treefile = $self->tempdir . "/outtree";
$self->throw("LVB did not create treefile correctly")
unless (-e $treefile);
#create the trees
my $in = Bio::TreeIO->new(-file => $treefile, '-format' => 'newick');
my @trees = ();
while (my $tree = $in->next_tree()) {
push @trees, $tree;
}
unless ( $self->save_tempfiles ) {
# Clean up the temporary files created along the way...
unlink $lvb_infile;
unlink $treefile;
}
return @trees;
}
=head2 _setinput
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for lvb program
Example :
Returns : name of file containing a multiple alignment in
Phylip 3.6 format
Args : SimpleAlign object reference or input file name
=cut
sub _setinput {
my ($self, $input, $suffix) = @_;
my ($alnfilename,$infilename, $temp, $tfh,$input_tmp,$input_fh);
# If $input is not a reference it better be the name of a
# file with the sequence/
# a phy formatted alignment file
unless (ref $input) {
# check that file exists or throw
$alnfilename= $input;
unless (-e $input) {return 0;}
return $alnfilename;
}
# $input may be a SimpleAlign Object
if ($input->isa("Bio::Align::AlignI")) {
# Open temporary file for both reading & writing of BioSeq array
($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir);
my $alnIO = Bio::AlignIO->new(-fh => $tfh, -format=>'phylip',idlength=>$10);
$alnIO->write_aln($input);
$alnIO->close();
close($tfh);
$tfh = undef;
unless ($self->format() =~ /^interleaved$/i) {
$self->warn("resetting LVB format to interleaved");
$self->format("interleaved");
}
return $alnfilename;
}
return 0;
}
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for lvb program
Example :
Returns : parameter string to be passed to LVB
Args : name of calling object
=cut
sub _setparams {
my ($attr, $value, $self);
$self = shift;
my $param_string = "";
for $attr (@LVB_PARAMS) {
$value = $self->$attr();
if ($attr =~/SEED/i) {
$value = "" unless defined $value;
$param_string .= "$value\n";
} elsif ($attr =~ /BOOTSTRAPS/i) {
$value = 0 unless defined $value;
$param_string .= "$value\n";
} else { # we want I for "interleaved" or S for "sequential",
# U for "unknown" or F for "fifthstate",
# F for "fast" or S for "slow"
$param_string .= uc(substr $value, 0, 1) . "\n";
}
}
return $param_string;
}
1; # Needed to keep compiler happy
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