Provided by: libbio-perl-run-perl_1.7.3-9_all 
NAME
Bio::Tools::Run::Alignment::Amap - Object for the calculation of an iterative multiple
sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0)
program
SYNOPSIS
# Build a muscle alignment factory
$factory = Bio::Tools::Run::Alignment::Amap->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.
#To run amap with training, try something like:
#First round to generate train.params
$factory = Bio::Tools::Run::Alignment::Amap->new
(
'iterative-refinement' => '1000',
'consistency' => '5',
'pre-training' => '20',
'emissions' => '',
'verbose' => '',
'train' => "$dir/$subdir/$outdir/train.params",
);
$factory->outfile_name("$dir/$subdir/$outdir/train.params");
#Second round to use train.params to get a high qual alignment
$seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref);
$aln = '';
$factory = '';
$factory = Bio::Tools::Run::Alignment::Amap->new
(
'iterative-refinement' => '1000',
'consistency' => '5',
'pre-training' => '20',
'verbose' => '',
'paramfile' => "$dir/$subdir/$outdir/train.params",
);
$factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
$aln = $factory->align($seq_array_ref);
DESCRIPTION
Amap uses a Sequence Annealing algorithm which is an incremental method for building
multiple alignments. You can get it and see information about it at this URL
http://bio.math.berkeley.edu/amap/
Helping the module find your executable
FIXME: Amap uses the same parameters as Probcons, plus a few others. I haven't had time to
check all the changes from the Probcons.pm runnable. Feel free to do it.
You will need to enable Amap to find the amap program. This can be done in (at least)
three ways:
1. Make sure the amap executable is in your path (i.e.
'which amap' returns a valid program
2. define an environmental variable AMAPDIR which points to a
directory containing the 'amap' app:
In bash
export AMAPDIR=/home/progs/amap or
In csh/tcsh
setenv AMAPDIR /home/progs/amap
3. include a definition of an environmental variable AMAPDIR
in every script that will
BEGIN {$ENV{AMAPDIR} = '/home/progs/amap'; }
use Bio::Tools::Run::Alignment::Amap;
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 - Albert Vilella
Email foo@bar.com
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 $amap = Bio::Tools::Run::Alignment::Amap->new();
Function: Constructor
Returns : Bio::Tools::Run::Alignment::Amap
Args : -outfile_name => $outname
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(\@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 amap program
Example :
Returns : nothing; amap 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 amap
_setinput
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for amap program
Example :
Returns : name of file containing amap 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 amap program
Example :
Returns : parameter string to be passed to amap
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 = $amap->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 : $amap->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