Provided by: libbio-perl-run-perl_1.6.9-2_all 
NAME
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
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.
Helping the module find your executable
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.
PARAMETERS FOR ALIGNMENT COMPUTATION
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).
IN
Title : IN
Description : (optional) input filename, this is specified when
align so should not use this directly unless one
understand TCoffee program very well.
TYPE
Title : TYPE
Args : [string] DNA, PROTEIN
Description : (optional) set the sequence type, guessed automatically
so should not use this directly
PARAMETERS
Title : PARAMETERS
Description : (optional) Indicates a file containing extra parameters
EXTEND
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_NORMALISE
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_MODE
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).
KTUPLE
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).
NDIAGS
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_MODE
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_MATRIX
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'
MATRIX
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
GAPOPEN
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.
GAPEXT
Title : GAPEXT
Args : numeric
Default : 0
Description : Indicates the penalty applied for extending a gap.
COSMETIC_PENALTY
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_MODE
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.
WEIGHT
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_ALIGN
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 OUTPUT
NEWTREE
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
USETREE
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_MODE
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.
QUICKTREE
Title : QUICKTREE
Args :
Default :
Description : This flag is kept for compatibility with ClustalW.
It indicates that: -tree_mode=very_fast
PARAMETERS FOR ALIGNMENT OUTPUT
OUTFILE
Title : OUTFILE
Args : out_aln file, default, no
Default : default ( yourseqfile.aln)
Description : indicates name of output alignment file
OUTPUT
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
CASE
Title : CASE
Args : upper, lower
Default : upper
Description : triggers choice of the case for output
CPU
Title : CPU
Args : value
Default : 0
Description : Indicates the cpu time (micro seconds) that must be
added to the t_coffee computation time.
OUT_LIB
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
OUTORDER
Title : OUTORDER
Args : input or aligned
Default : input
Description : Sets the name of the library output. Default implies
<run_name>.tc_lib
SEQNOS
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 OUTPUT
RUN_NAME
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.
ALIGN
Title : ALIGN
Args :
Default :
Description : Indicates that the program must produce the
alignment. This flag is here for compatibility with
ClustalW
QUIET
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.
CONVERT
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).
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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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 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 - Jason Stajich, Peter Schattner
Email jason-at-bioperl-dot-org, schattner@alum.mit.edu
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 : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
error_string
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)
version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
run
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
align
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_align
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.
_run
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
_setinput
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
_setparams
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
aformat
Title : aformat
Usage : my $alignmentformat = $self->aformat();
Function: Get/Set alignment format
Returns : string
Args : string
methods
Title : methods
Usage : my @methods = $self->methods()
Function: Get/Set Alignment methods - NOT VALIDATED
Returns : array of strings
Args : arrayref of strings
Bio::Tools::Run::BaseWrapper 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 = $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
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 : $tcoffee->cleanup();
Function: Will cleanup the tempdir directory
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