Bio::Tools::Run::Alignment TCoffee
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Summary
Bio::Tools::Run::Alignment::TCoffee - Object for the calculation of a
multiple sequence alignment from a set of unaligned sequences or
alignments using the TCoffee program
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Factory::ApplicationFactoryI
Bio::Root::IO
Bio::Seq
Bio::SeqIO
Bio::SimpleAlign
Bio::Tools::Run::WrapperBase
Cwd
Inherit
Bio::Factory::ApplicationFactoryI Bio::Tools::Run::WrapperBase
Synopsis
  # Build a tcoffee alignment factory
@params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
$factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
# Pass the factory a list of sequences to be aligned. $inputfilename = 't/cysprot.fa'; # $aln is a SimpleAlign object. $aln = $factory->align($inputfilename); # or where @seq_array is an array of Bio::Seq objects $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); # Or one can pass the factory a pair of (sub)alignments #to be aligned against each other, e.g.: # where $aln1 and $aln2 are Bio::SimpleAlign objects. $aln = $factory->profile_align($aln1,$aln2); # Or one can pass the factory an alignment and one or more # unaligned sequences to be added to the alignment. For example: # $seq is a Bio::Seq object. $aln = $factory->profile_align($aln1,$seq); #There are various additional options and input formats available. #See the DESCRIPTION section that follows for additional details.
Description
Note: this DESCRIPTION only documents the (Bio)perl interface to
TCoffee. You will need to enable TCoffee to find the t_coffee program. This
can be done in (at least) three ways:
 1. Make sure the t_coffee executable is in your path so that
which t_coffee returns a t_coffee executable on your system.
2. Define an environmental variable TCOFFEEDIR which is a dir which contains the 't_coffee' app: In bash export TCOFFEEDIR=/home/username/progs/T-COFFEE_distribution_Version_1.37/bin In csh/tcsh setenv TCOFFEEDIR /home/username/progs/T-COFFEE_distribution_Version_1.37/bin 3. Include a definition of an environmental variable TCOFFEEDIR in every script that will use this TCoffee wrapper module. BEGIN { $ENV{TCOFFEDIR} = '/home/username/progs/T-COFFEE_distribution_Version_1.37/bin' } use Bio::Tools::Run::Alignment::TCoffee;
If you are running an application on a webserver make sure the
webserver environment has the proper PATH set or use the options 2 or
3 to set the variables.
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
new
No description
Code
AUTOLOAD
No description
Code
error_stringDescriptionCode
versionDescriptionCode
runDescriptionCode
alignDescriptionCode
profile_alignDescriptionCode
_runDescriptionCode
_setinputDescriptionCode
_setparamsDescriptionCode
aformatDescriptionCode
methodsDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
error_stringcodeprevnextTop
 Title   : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysus run is stored.
Returns : value of error_string
Args : newvalue (optional)
versioncodeprevnextTop
 Title   : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
runcodeprevnextTop
 Title   : run
Usage : my $output = $application->run(-seq => $seq,
-profile => $profile,
-type => 'profile-aln');
Function: Generic run of an application
Returns : Bio::SimpleAlign object
Args : key-value parameters allowed for TCoffee runs AND
-type => profile-aln or alignment for profile alignments or
just multiple sequence alignment
-seq => either Bio::PrimarySeqI object OR
array ref of Bio::PrimarySeqI objects OR
filename of sequences to run with
-profile => profile to align to, if this is an array ref
will specify the first two entries as the two
profiles to align to each other
aligncodeprevnextTop
 Title   : align
Usage :
$inputfilename = 't/data/cysprot.fa';
$aln = $factory->align($inputfilename);
or
$seq_array_ref = \@seq_array;
# @seq_array is array of Seq objs
$aln = $factory->align($seq_array_ref);
Function: Perform a multiple sequence alignment
Returns : Reference to a SimpleAlign object containing the
sequence alignment.
Args : Name of a file containing a set of unaligned fasta sequences
or else an array of references to Bio::Seq objects.
Throws an exception if argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. If argument is string, throws exception if file corresponding to string name can not be found. If argument is Bio::Seq array, throws exception if less than two sequence objects are in array.
profile_aligncodeprevnextTop
 Title   : profile_align
Usage :
Function: Perform an alignment of 2 (sub)alignments
Example :
Returns : Reference to a SimpleAlign object containing the (super)alignment.
Args : Names of 2 files containing the subalignments
or references to 2 Bio::SimpleAlign objects.
Note : Needs to be updated to run with newer TCoffee code, which
allows more than two profile alignments.

Throws an exception if arguments are not either strings (eg filenames)
or references to SimpleAlign objects.
_runcodeprevnextTop
 Title   :  _run
Usage : Internal function, not to be called directly
Function: makes actual system call to tcoffee program
Example :
Returns : nothing; tcoffee output is written to a
temporary file OR specified output file
Args : Name of a file containing a set of unaligned fasta sequences
and hash of parameters to be passed to tcoffee
_setinputcodeprevnextTop
 Title   :  _setinput
Usage : Internal function, not to be called directly
Function: Create input file for tcoffee program
Example :
Returns : name of file containing tcoffee data input AND
type of file (if known, S for sequence, L for sequence library,
A for sequence alignment)
Args : Seq or Align object reference or input file name
_setparamscodeprevnextTop
 Title   :  _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for tcoffee program
Example :
Returns : parameter string to be passed to tcoffee
during align or profile_align
Args : name of calling object
aformatcodeprevnextTop
 Title   : aformat
Usage : my $alignmentformat = $self->aformat();
Function: Get/Set alignment format
Returns : string
Args : string
methodscodeprevnextTop
 Title   : methods
Usage : my @methods = $self->methods()
Function: Get/Set Alignment methods - NOT VALIDATED
Returns : array of strings
Args : arrayref of strings
Methods code
BEGINTop
BEGIN {
    $PROGRAM_NAME = 't_coffee';
    $PROGRAM_DIR = $ENV{'TCOFFEEDIR'};
    %DEFAULTS = ( 'MATRIX' => 'blosum',
                  'OUTPUT' => 'clustalw',
                  'AFORMAT'=> 'msf',
                  'METHODS' => [qw(lalign_id_pair clustalw_pair)]
                );


    @TCOFFEE_PARAMS = qw(IN TYPE PARAMETERS DO_NORMALISE EXTEND
			 DP_MODE KTUPLE NDIAGS DIAG_MODE SIM_MATRIX
			 MATRIX GAPOPEN GAPEXT COSMETIC_PENALTY TG_MODE
			 WEIGHT SEQ_TO_ALIGN NEWTREE USETREE TREE_MODE
			 OUTFILE OUTPUT CASE CPU OUT_LIB OUTORDER SEQNOS
			 RUN_NAME CONVERT 
                         );

    @TCOFFEE_SWITCHES = qw(QUICKTREE);

    @OTHER_SWITCHES = qw(QUIET ALIGN KEEPDND);

# Authorize attribute fields
foreach my $attr ( @TCOFFEE_PARAMS, @TCOFFEE_SWITCHES, @OTHER_SWITCHES ) { $OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
    return $PROGRAM_NAME;
}
program_dirdescriptionprevnextTop
sub program_dir {
    return $PROGRAM_DIR;
}
newdescriptionprevnextTop
sub new {
	my ($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
$self->$attr($value); } $self->matrix($DEFAULTS{'MATRIX'}) unless( $self->matrix ); $self->output($DEFAULTS{'OUTPUT'}) unless( $self->output ); $self->methods($DEFAULTS{'METHODS'}) unless $self->methods; # $self->aformat($DEFAULTS{'AFORMAT'}) unless $self->aformat;
return $self;
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    # aliasing
$attr = 'OUTFILE' if $attr eq 'OUTFILE_NAME'; $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr}; $self->{$attr} = shift if @_; return $self->{$attr};
}
error_stringdescriptionprevnextTop
sub error_string {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};
}
versiondescriptionprevnextTop
sub version {
    my ($self) = @_;
    my $exe;
    return undef unless $exe = $self->executable;
    my $string = `$exe -quiet=stdout 2>&1` ;
    $string =~ /Version_([\d.]+)/;
    return $1 || undef;
}
rundescriptionprevnextTop
sub run {
   my ($self,@args) = @_;
   my ($type,$seq,$profile) = $self->_rearrange([qw(TYPE
						    SEQ
						    PROFILE)],
						@args);
   if( $type =~ /align/i ) {
       return $self->align($seq);
   } elsif( $type =~ /profile/i ) {
       return $self->profile_align($profile,$seq);
   } else { 
       $self->warn("unrecognized alignment type $type\n");
   }
   return undef;
}
aligndescriptionprevnextTop
sub align {
    my ($self,$input) = @_;
    # Create input file pointer
$self->io->_io_cleanup(); my ($infilename,$type) = $self->_setinput($input); if (!$infilename) { $self->throw("Bad input data or less than 2 sequences in $input !"); } my $param_string = $self->_setparams(); # run tcoffee
return $self->_run('align', [$infilename,$type], $param_string); } #################################################
}
profile_aligndescriptionprevnextTop
sub profile_align {
    my $self = shift;
    my $input1 = shift;
    my $input2 = shift;
    
    my ($temp,$infilename1,$infilename2,$type1,$type2,$input,$seq);

    $self->io->_io_cleanup();
    # Create input file pointers
($infilename1,$type1) = $self->_setinput($input1); ($infilename2,$type2) = $self->_setinput($input2); unless ($type1) { $self->throw("Unknown type for first argument"); } unless ($type2) { $self->throw("Unknown type for second argument") } if (!$infilename1 || !$infilename2) { $self->throw("Bad input data: $input1 or $input2 !"); } my $param_string = $self->_setparams(); # run tcoffee
my $aln = $self->_run('profile-aln', [$infilename1,$type1], [$infilename2,$type2], $param_string) ; } #################################################
}
_rundescriptionprevnextTop
sub _run {
    my ($infilename, $infile1,$infile2) = ('','','');
    my $self = shift;
    my $command = shift;
    my $instring;
    if ($command =~ /align/) {
        my $infile = shift ;
        my $type;
        ($infilename,$type) = @$infile;
        $instring =  '-in='.join(',',($infilename, 'X'.$self->matrix,
                          $self->methods));
    }
    if ($command =~ /profile/) {
        my $in1 = shift ;
        my $in2 = shift ;
        my ($type1,$type2);
        ($infile1,$type1) = @$in1;
        ($infile2,$type2) = @$in2;
        # in later versions (tested on 5.72 and 7.54) the API for profile
# alignment changed. This attempts to do the right thing for older
# versions but corrects for newer ones
if ($self->version && $self->version < 5) { # this breaks severely on newer TCoffee (>= v5)
unless (($self->matrix =~ /none/i) || ($self->matrix =~ /null/i) ) { $instring = '-in='.join(',', ($type2.$infile2), 'X'.$self->matrix, (map {'M'.$_} $self->methods) ); $instring .= ' -profile='.$infile1; } else { $instring = '-in='.join(',',( $type1.$infile1, $type2.$infile2, (map {'M'.$_} $self->methods) ) ); } } else { if ($type2 eq 'S') { # second infile is a sequence, not an alignment
$instring .= ' -profile='.join(',',$infile1); $instring .= ' -seq='.join(',',$infile2); } else { $instring .= ' -profile='.join(',',$infile1,$infile2); } $instring .= ' -matrix='.$self->matrix unless (($self->matrix =~ /none/i) || ($self->matrix =~ /null/i)) ; $instring .= ' -method='.join(',',$self->methods) if ($self->methods) ; } } my $param_string = shift; # my ($paramfh,$parameterFile) = $self->io->tempfile;
# print $paramfh ( "$instring\n-output=gcg$param_string") ;
# close($paramfh);
# my $commandstring = "t_coffee -output=gcg -parameters $parameterFile" ; ##MJL
my $commandstring = $self->executable." $instring $param_string"; #$self->debug( "tcoffee command = $commandstring \n");
my $status = system($commandstring); my $outfile = $self->outfile(); if( !-e $outfile || -z $outfile ) { $self->warn( "TCoffee call crashed: $? [command $commandstring]\n"); return undef; } # retrieve alignment (Note: MSF format for AlignIO = GCG format of
# tcoffee)
my $in = Bio::AlignIO->new('-file' => $outfile, '-format' => $self->output); my $aln = $in->next_aln(); # Replace file suffix with dnd to find name of dendrogram file(s) to delete
if( ! $self->keepdnd ) { foreach my $f ( $infilename, $infile1, $infile2 ) { next if( !defined $f || $f eq ''); $f =~ s/\.[^\.]*$// ; # because TCoffee writes these files to the CWD
if( $Bio::Root::IO::PATHSEP ) { my @line = split(/$Bio::Root::IO::PATHSEP/, $f); $f = pop @line; } else { (undef, undef, $f) = File::Spec->splitpath($f); } unlink $f .'.dnd' if( $f ne '' ); } } return $aln;
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    #  If $input is not a reference it better be the name of a
# file with the sequence/ alignment data...
my $type = ''; if (! ref $input) { # check that file exists or throw
$infilename = $input; unless (-e $input) {return 0;} # let's peek and guess
open(my $IN,$infilename) || $self->throw("Cannot open $infilename"); my $header = <$IN>; if( $header =~ /^\s+\d+\s+\d+/ || $header =~ /Pileup/i || $header =~ /clustal/i ) { # phylip
$type = 'A'; } # On some systems, having filenames with / in them (ie. a file in a
# directory) causes t-coffee to completely fail. It warns on all systems.
# The -no_warning option solves this, but there is still some strange
# bug when doing certain profile-related things. This is magically solved
# by copying the profile file to a temp file in the current directory, so
# it its filename supplied to t-coffee contains no /
# (It's messy here - I just do this to /all/ input files to most easily
# catch all variants of providing a profile - it may only be the last
# form (isa("Bio::PrimarySeqI")) that causes a problem?)
my (undef, undef, $adjustedfilename) = File::Spec->splitpath($infilename); if ($adjustedfilename ne $infilename) { my ($fh, $tempfile) = $self->io->tempfile(-dir => cwd()); seek($IN, 0, 0); while (<$IN>) { print $fh $_; } close($fh); (undef, undef, $tempfile) = File::Spec->splitpath($tempfile); $infilename = $tempfile; $type = 'S'; } close($IN); return ($infilename,$type); } elsif (ref($input) =~ /ARRAY/i ) { # $input may be an array of BioSeq objects...
# Open temporary file for both reading & writing of array
($tfh,$infilename) = $self->io->tempfile(-dir => cwd()); (undef, undef, $infilename) = File::Spec->splitpath($infilename); if( ! ref($input->[0]) ) { $self->warn("passed an array ref which did not contain objects to _setinput"); return undef; } elsif( $input->[0]->isa('Bio::PrimarySeqI') ) { $temp = Bio::SeqIO->new('-fh' => $tfh, '-format' => 'fasta'); my $ct = 1; foreach $seq (@$input) { return 0 unless ( ref($seq) && $seq->isa("Bio::PrimarySeqI") ); if( ! defined $seq->display_id || $seq->display_id =~ /^\s+$/) { $seq->display_id( "Seq".$ct++); } $temp->write_seq($seq); } $temp->close(); undef $temp; close($tfh); $tfh = undef; $type = 'S'; } elsif( $input->[0]->isa('Bio::Align::AlignI' ) ) { $temp = Bio::AlignIO->new('-fh' => $tfh, '-format' => $self->aformat); foreach my $aln (@$input) { next unless ( ref($aln) && $aln->isa("Bio::Align::AlignI") ); $temp->write_aln($aln); } $temp->close(); undef $temp; close($tfh); $tfh = undef; $type = 'A'; } else { $self->warn( "got an array ref with 1st entry ". $input->[0]. " and don't know what to do with it\n"); } return ($infilename,$type); # $input may be a SimpleAlign object.
} elsif ( $input->isa("Bio::Align::AlignI") ) { # Open temporary file for both reading & writing of SimpleAlign object
($tfh, $infilename) = $self->io->tempfile(-dir => cwd()); (undef, undef, $infilename) = File::Spec->splitpath($infilename); $temp = Bio::AlignIO->new(-fh=>$tfh, '-format' => 'clustalw'); $temp->write_aln($input); close($tfh); undef $tfh; return ($infilename,'A'); } # or $input may be a single BioSeq object (to be added to
# a previous alignment)
elsif ( $input->isa("Bio::PrimarySeqI")) { # Open temporary file for both reading & writing of BioSeq object
($tfh,$infilename) = $self->io->tempfile(-dir => cwd()); (undef, undef, $infilename) = File::Spec->splitpath($infilename); $temp = Bio::SeqIO->new(-fh=> $tfh, '-format' =>'Fasta'); $temp->write_seq($input); $temp->close(); close($tfh); undef $tfh; return ($infilename,'S'); } else { $self->warn("Got $input and don't know what to do with it\n"); } return 0;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($self) = @_;
    my ($attr, $value,$param_string);
    $param_string = '';
    my $laststr;
    for  $attr ( @TCOFFEE_PARAMS ) {
	$value = $self->$attr();
	next unless (defined $value);	
	my $attr_key = lc $attr;
	if( $attr_key =~ /matrix/ ) {
	    $self->{'_in'} = [ "X".lc($value) ];
	} else {
	    $attr_key = ' -'.$attr_key;
	    $param_string .= $attr_key .'='.$value;
	}
   }
    for  $attr ( @TCOFFEE_SWITCHES) {
	$value = $self->$attr();
	next unless ($value);
	my $attr_key = lc $attr; #put switches in format expected by tcoffee
$attr_key = ' -'.$attr_key; $param_string .= $attr_key ; } # Set default output file if no explicit output file selected
unless ($self->outfile ) { my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir()); close($tfh); undef $tfh; $self->outfile($outfile); $param_string .= " -outfile=$outfile" ; } if ($self->quiet() || $self->verbose < 0) { $param_string .= ' -quiet';} # -no_warning is required on some systems with certain versions or failure
# is guaranteed
if ($self->version >= 4 && $self->version < 4.7) { $param_string .= ' -no_warning'; } return $param_string;
}
aformatdescriptionprevnextTop
sub aformat {
    my $self = shift;
    $self->{'_aformat'} = shift if @_;
    return $self->{'_aformat'};
}
methodsdescriptionprevnextTop
sub methods {
   my ($self) = shift;

   @{$self->{'_methods'}} = @{shift || []} if @_;
   return @{$self->{'_methods'} || []};
}
General documentation
PARAMETERS FOR ALIGNMENT COMPUTATIONTop
There are a number of possible parameters one can pass in TCoffee.
One should really read the online manual for the best explanation of
all the features. See
http://igs-server.cnrs-mrs.fr/~cnotred/Documentation/t_coffee/t_coffee_doc.html
These can be specified as parameters when instantiating a new TCoffee
object, or through get/set methods of the same name (lowercase).
INTop
 Title       : IN
Description : (optional) input filename, this is specified when
align so should not use this directly unless one
understand TCoffee program very well.
TYPETop
 Title       : TYPE
Args : [string] DNA, PROTEIN
Description : (optional) set the sequence type, guessed automatically
so should not use this directly
PARAMETERSTop
 Title       : PARAMETERS
Description : (optional) Indicates a file containing extra parameters
EXTENDTop
 Title       : EXTEND
Args : 0, 1, or positive value
Default : 1
Description : Flag indicating that library extension should be
carried out when performing multiple alignments, if set
to 0 then extension is not made, if set to 1 extension
is made on all pairs in the library. If extension is
set to another positive value, the extension is only
carried out on pairs having a weigth value superior to
the specified limit.
DP_NORMALISETop
 Title       : DP_NORMALISE
Args : 0 or positive value
Default : 1000
Description : When using a value different from 0, this flag sets the
score of the highest scoring pair to 1000.
DP_MODETop
 Title       : DP_MODE
Args : [string] gotoh_pair_wise, myers_miller_pair_wise,
fasta_pair_wise cfasta_pair_wise
Default : cfast_fair_wise
Description : Indicates the type of dynamic programming used by
the program
gotoh_pair_wise : implementation of the gotoh algorithm (quadratic in memory and time) myers_miller_pair_wise : implementation of the Myers and Miller dynamic programming algorithm ( quadratic in time and linear in space). This algorithm is recommended for very long sequences. It is about 2 time slower than gotoh. It only accepts tg_mode=1. fasta_pair_wise: implementation of the fasta algorithm. The sequence is hashed, looking for ktuples words. Dynamic programming is only carried out on the ndiag best scoring diagonals. This is much faster but less accurate than the two previous. cfasta_pair_wise : c stands for checked. It is the same algorithm. The dynamic programming is made on the ndiag best diagonals, and then on the 2*ndiags, and so on until the scores converge. Complexity will depend on the level of divergence of the sequences, but will usually be L*log(L), with an accuracy comparable to the two first mode ( this was checked on BaliBase).
KTUPLETop
 Title       : KTUPLE
Args : numeric value
Default : 1 or 2 (1 for protein, 2 for DNA )
Description : Indicates the ktuple size for cfasta_pair_wise dp_mode and fasta_pair_wise. It is set to 1 for proteins, and 2 for DNA. The alphabet used for protein is not the 20 letter code, but a mildly degenerated version, where some residues are grouped under one letter, based on physicochemical properties: rk, de, qh, vilm, fy (the other residues are not degenerated).
NDIAGSTop
 Title       : NDIAGS
Args : numeric value
Default : 0
Description : Indicates the number of diagonals used by the
fasta_pair_wise algorithm. When set to 0,
n_diag=Log (length of the smallest sequence)
DIAG_MODETop
 Title       : DIAG_MODE
Args : numeric value
Default : 0
Description : Indicates the manner in which diagonals are scored during the fasta hashing. 0 indicates that the score of a diagonal is equal to the sum of the scores of the exact matches it contains. 1 indicates that this score is set equal to the score of the best uninterrupted segment 1 can be useful when dealing with fragments of sequences.
SIM_MATRIXTop
 Title       : SIM_MATRIX
Args : string
Default : vasiliky
Description : Indicates the manner in which the amino acid is being
degenerated when hashing. All the substitution matrix
are acceptable. Categories will be defined as sub-group
of residues all having a positive substitution score
(they can overlap).
If you wish to keep the non degenerated amino acid alphabet, use 'idmat'
MATRIXTop
 Title       : MATRIX
Args :
Default :
Description : This flag is provided for compatibility with
ClustalW. Setting matrix = 'blosum' is equivalent to
-in=Xblosum62mt , -matrix=pam is equivalent to
in=Xpam250mt . Apart from this, the rules are similar
to those applying when declaring a matrix with the
-in=X fl
GAPOPENTop
 Title       : GAPOPEN
Args : numeric
Default : 0
Description : Indicates the penalty applied for opening a gap. The
penalty must be negative. If you provide a positive
value, it will automatically be turned into a negative
number. We recommend a value of 10 with pam matrices,
and a value of 0 when a library is used.
GAPEXTTop
 Title       : GAPEXT
Args : numeric
Default : 0
Description : Indicates the penalty applied for extending a gap.
COSMETIC_PENALTYTop
 Title       : COSMETIC_PENALTY
Args : numeric
Default : 100
Description : Indicates the penalty applied for opening a gap. This
penalty is set to a very low value. It will only have
an influence on the portions of the alignment that are
unalignable. It will not make them more correct, but
only more pleasing to the eye ( i.e. Avoid stretches of
lonely residues).
The cosmetic penalty is automatically turned off if a substitution matrix is used rather than a library.
TG_MODETop
 Title       : TG_MODE
Args : 0,1,2
Default : 1
Description : (Terminal Gaps)
0: indicates that terminal gaps must be panelized with
a gapopen and a gapext penalty.
1: indicates that terminal gaps must be penalized only
with a gapext penalty
2: indicates that terminal gaps must not be penalized.
WEIGHTTop
 Title       : WEIGHT
Args : sim or sim_<matrix_name or matrix_file> or integer value
Default : sim
Description : Weight defines the way alignments are weighted when turned into a library. sim indicates that the weight equals the average identity within the match residues. sim_matrix_name indicates the average identity with two residues regarded as identical when their substitution value is positive. The valid matrices names are in matrices.h (pam250mt) . Matrices not found in this header are considered to be filenames. See the format section for matrices. For instance, -weight=sim_pam250mt indicates that the grouping used for similarity will be the set of classes with positive substitutions. Other groups include sim_clustalw_col ( categories of clustalw marked with :) sim_clustalw_dot ( categories of clustalw marked with .) Value indicates that all the pairs found in the alignments must be given the same weight equal to value. This is useful when the alignment one wishes to turn into a library must be given a pre-specified score (for instance if they come from a structure super-imposition program). Value is an integer: -weight=1000 Note : Weight only affects methods that return an alignment to T-Coffee, such as ClustalW. On the contrary, the version of Lalign we use here returns a library where weights have already been applied and are therefore insensitive to the -weight flag.
SEQ_TO_ALIGNTop
 Title       : SEQ_TO_ALIGN
Args : filename
Default : no file - align all the sequences
Description : You may not wish to align all the sequences brought in by the -in flag. Supplying the seq_to_align flag allows for this, the file is simply a list of names in Fasta format. However, note that library extension will be carried out on all the sequences.
PARAMETERS FOR TREE COMPUTATION AND OUTPUTTop
NEWTREETop
 Title       : NEWTREE
Args : treefile
Default : no file
Description : Indicates the name of the new tree to compute. The
default will be <sequence_name>.dnd, or <run_name.dnd>.
Format is Phylip/Newick tree format
USETREETop
 Title       : USETREE
Args : treefile
Default : no file specified
Description : This flag indicates that rather than computing a new
dendrogram, t_coffee can use a pre-computed one. The
tree files are in phylips format and compatible with
ClustalW. In most cases, using a pre-computed tree will
halve the computation time required by t_coffee. It is
also possible to use trees output by ClustalW or
Phylips. Format is Phylips tree format
TREE_MODETop
 Title       : TREE_MODE
Args : slow, fast, very_fast
Default : very_fast
Description : This flag indicates the method used for computing the
dendrogram.
slow : the chosen dp_mode using the extended library,
fast : The fasta dp_mode using the extended library.
very_fast: The fasta dp_mode using pam250mt.
QUICKTREETop
 Title       : QUICKTREE
Args :
Default :
Description : This flag is kept for compatibility with ClustalW.
It indicates that: -tree_mode=very_fast
PARAMETERS FOR ALIGNMENT OUTPUTTop
OUTFILETop
 Title       : OUTFILE
Args : out_aln file, default, no
Default : default ( yourseqfile.aln)
Description : indicates name of output alignment file
OUTPUTTop
 Title       : OUTPUT
Args : format1, format2
Default : clustalw
Description : Indicated format for outputting outputfile
Supported formats are:
clustalw_aln, clustalw: ClustalW format. gcg, msf_aln : Msf alignment. pir_aln : pir alignment. fasta_aln : fasta alignment. phylip : Phylip format. pir_seq : pir sequences (no gap). fasta_seq : fasta sequences (no gap). As well as: score_html : causes the output to be a reliability plot in HTML score_pdf : idem in PDF. score_ps : idem in postscript. More than one format can be indicated: -output=clustalw,gcg, score_html
CASETop
 Title       : CASE
Args : upper, lower
Default : upper
Description : triggers choice of the case for output
CPUTop
 Title       : CPU
Args : value
Default : 0
Description : Indicates the cpu time (micro seconds) that must be
added to the t_coffee computation time.
OUT_LIBTop
 Title       : OUT_LIB
Args : name of library, default, no
Default : default
Description : Sets the name of the library output. Default implies
<run_name>.tc_lib
OUTORDERTop
 Title       : OUTORDER
Args : input or aligned
Default : input
Description : Sets the name of the library output. Default implies
<run_name>.tc_lib
SEQNOSTop
 Title       : SEQNOS
Args : on or off
Default : off
Description : Causes the output alignment to contain residue numbers
at the end of each line:
PARAMETERS FOR GENERIC OUTPUTTop
RUN_NAMETop
 Title       : RUN_NAME
Args : your run name
Default :
Description : This flag causes the prefix <your sequences> to be
replaced by <your run name> when renaming the default
files.
ALIGNTop
 Title       : ALIGN
Args :
Default :
Description : Indicates that the program must produce the
alignment. This flag is here for compatibility with
ClustalW
QUIETTop
 Title       : QUIET
Args : stderr, stdout, or filename, or nothing
Default : stderr
Description : Redirects the standard output to either a file.
-quiet on its own redirect the output to /dev/null.
CONVERTTop
 Title       : CONVERT
Args :
Default :
Description : Indicates that the program must not compute the
alignment but simply convert all the sequences,
alignments and libraries into the format indicated with
-output. This flag can also be used if you simply want
to compute a library ( i.e. You have an alignment and
you want to turn it into a library).
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/
AUTHOR - Jason Stajich, Peter SchattnerTop
Email jason-at-bioperl-dot-org, schattner@alum.mit.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Bio::Tools::Run::BaseWrapper methodsTop
no_param_checksTop
 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_tempfilesTop
 Title   : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
outfile_nameTop
 Title   : outfile_name
Usage : my $outfile = $tcoffee->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
tempdirTop
 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
cleanupTop
 Title   : cleanup
Usage : $tcoffee->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
ioTop
 Title   : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO
Args : none