| Bio::Tools::Run::Alignment::Amap(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Alignment::Amap(3pm) |
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
# 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);
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/
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;
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
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.
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:
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Email foo@bar.com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : new Usage : my $amap = Bio::Tools::Run::Alignment::Amap->new(); Function: Constructor Returns : Bio::Tools::Run::Alignment::Amap Args : -outfile_name => $outname
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none
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
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.
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
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
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
Title : aformat Usage : my $alignmentformat = $self->aformat(); Function: Get/Set alignment format Returns : string Args : string
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)
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)
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
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
Title : cleanup Usage : $amap->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none
| 2018-09-14 | perl v5.26.2 |