SYNOPSIS
# Build a kalign alignment factory
$factory = Bio::Tools::Run::Alignment::Kalign->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.:
#There are various additional options and input formats available.
#See the DESCRIPTION section that follows for additional details.
DESCRIPTION
Please cite:
Timo Lassmann and Erik L.L. Sonnhammer (2005)
Kalign - an accurate and fast multiple sequence alignment algorithm.
BMC Bioinformatics 6:298
Helping the module find your executable
You will need to enable Kalign to find the kalign program. This can be done in (at least) three ways:
1. Make sure the kalign executable is in your path (i.e.
'which kalign' returns a valid program
2. define an environmental variable KALIGNDIR which points to a
directory containing the 'kalign' app:
In bash
export KALIGNDIR=/home/progs/kalign or
In csh/tcsh
setenv KALIGNDIR /home/progs/kalign
3. include a definition of an environmental variable KALIGNDIR
in every script that will
BEGIN {$ENV{KALIGNDIR} = '/home/progs/kalign'; }
use Bio::Tools::Run::Alignment::Kalign;
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 - Albert Vilella
Email [email protected]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 :
new
Title : new Usage : my $kalign = Bio::Tools::Run::Alignment::Kalign->new(); Function: Constructor Returns : Bio::Tools::Run::Alignment::Kalign Args : -outfile_name => $outname
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() < 2 Function: Determine the version number of the program Example : Returns : float or undef Args : none
run
Title : run
Usage : my $output = $application->run(\@seqs);
Function: Generic run of an application
Returns : Bio::SimpleAlign object
Args : Arrayref of Bio::PrimarySeqI objects or
a filename to run on
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.
_run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to kalign program
Example :
Returns : nothing; kalign 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 kalign
_setinput
Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for kalign program Example : Returns : name of file containing kalign data input AND Args : Arrayref of Seqs or input file name
_setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for kalign program
Example :
Returns : parameter string to be passed to kalign
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
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 = $kalign->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 : $kalign->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