Bio::Tools::Run::Phylo LVB
Included librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Root::IO
Bio::Root::Root
Bio::SimpleAlign
Bio::Tools::Run::WrapperBase
Bio::TreeIO
Cwd
File::Copy
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
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");
Description
Wrapper for LVB, which uses a simulated annealing heuristic search
to seek parsimonious trees from a nucleotide multiple alignment.
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
new
No description
Code
AUTOLOAD
No description
Code
runDescriptionCode
create_treeDescriptionCode
_runDescriptionCode
_setinputDescriptionCode
_setparamsDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : ->program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : ->program_dir()
Function: returns undef
Args :
run codeprevnextTop
 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 Bio::Tree objects
Args : Name of a file containing a nucleotide multiple
alignment in Phylip 3.6 format, or a SimpleAlign
object
create_treecodeprevnextTop
 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 Bio::Tree objects
Args : Name of a file containing a nucleotide multiple
alignment in Phylip 3.6 format, or a SimpleAlign
object
_runcodeprevnextTop
 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
_setinputcodeprevnextTop
 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
_setparamscodeprevnextTop
 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
Methods code
BEGINTop
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}++;
}
program_namedescriptionprevnextTop
sub program_name {
            return 'lvb';
}
program_dirdescriptionprevnextTop
sub program_dir {
    return undef;
}
newdescriptionprevnextTop
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;
}
AUTOLOADdescriptionprevnextTop
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};
}
rundescriptionprevnextTop
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);
}
create_treedescriptionprevnextTop
sub create_tree {
  return shift->run(@_);
}

#################################################
}
_rundescriptionprevnextTop
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() || $self->verbose() < 0) { open(LVB_PIPE,"|".$self->executable.">/dev/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 $treefile; } return @trees;
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($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 $alnfilename; } return 0;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($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
}
General documentation
NAME Top
Bio::Tools::Run::Phylo::LVB - Object for using the LVB program to create
an array of Bio::Tree objects from a nucleotide multiple alignment
file or a nucleotide SimpleAlign object. Works with LVB version 2.1.
FEEDBACKTop
Mailing ListsTop
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
Support Top
 
Please direct usage questions or support issues to the mailing list:

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.
Reporting BugsTop
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://bugzilla.open-bio.org/
PARAMETERS FOR LVB COMPUTATIONTop
FORMATTop
  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".
GAPSTop
  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".
SEEDTop
  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.
DURATIONTop
  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".
BOOTSTRAPSTop
  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.
AUTHORTop
Daniel Barker
CONTRIBUTORSTop
Email jason-AT-bioperl_DOT_org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _