Bio::Tools::Run::AlignUser:Contributed PerBio::Tools::Run::Alignment::Proda(3)NAMEBio::Tools::Run::Alignment::Proda - Object for the calculation of sets
of multiple sequence alignments from a set of unaligned sequences or
alignments using the Proda program.
SYNOPSIS
# Build a Proda alignment factory
$factory = Bio::Tools::Run::Alignment::Proda->new(@params);
# Pass the factory a list of sequences to be aligned.
$inputfilename = 't/cysprot.fa';
# @alns is an array of SimpleAlign objects.
@alns = $factory->align($inputfilename);
# or where @seq_array is an array of Bio::Seq objects
$seq_array_ref = \@seq_array;
@alns = $factory->align($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.
$factory = Bio::Tools::Run::Alignment::Proda->new();
@alns = $factory->align($seq_array_ref);
DESCRIPTION
You can get it and see information about it at this URL
http://proda.stanford.edu
This program will return one or more local alignments for the different
repeated or rearranged regions in the sequences. If a sequences
contains more than one of those patterns, it will be present more than
once in the alignment. The difference will be in that the id contain
the start and end, like myseqid(123-456) and myseqid(567-890), instead
of simply myseqid as in the original input file. This is true for all
the output ids, even if they are present only once.
Helping the module find your executable
You will need to enable Proda to find the proda program. This can be
done in (at least) three ways:
1. Make sure the proda executable is in your path (i.e.
'which proda' returns a valid program
2. define an environmental variable PRODADIR which points to a
directory containing the 'proda' app:
In bash
export PRODADIR=/home/progs/proda or
In csh/tcsh
setenv PRODADIR /home/progs/proda
3. include a definition of an environmental variable PRODADIR
in every script that will
BEGIN {$ENV{PRODADIR} = '/home/progs/proda'; }
use Bio::Tools::Run::Alignment::Proda;
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://bugzilla.open-bio.org/
AUTHOR - Albert Vilella
Email avilella-at-gmail-dot-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 $proda = Bio::Tools::Run::Alignment::Proda->new();
Function: Constructor
Returns : Bio::Tools::Run::Alignment::Proda
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() < 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 proda program
Example :
Returns : nothing; proda 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 proda
_setinput
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for proda program
Example :
Returns : name of file containing proda 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 proda program
Example :
Returns : parameter string to be passed to proda
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 = $proda->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 : $proda->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
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