/ 
BioPerl-Run-1.007002
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Minimo

NAME

Bio::Tools::Run::Minimo - Wrapper for local execution of the Minimo assembler

SYNOPSIS

use Bio::Tools::Run::Minimo;
# Run Minmo using an input FASTA file
my $factory = Bio::Tools::Run::Minimo->new( -minimum_overlap_length => 35 );
my $asm_obj = $factory->run($fasta_file, $qual_file);
# An assembly object is returned by default
for my $contig ($assembly->all_contigs) {
  ... do something ...
}

# Read some sequences
use Bio::SeqIO;
my $sio = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta');
my @seqs;
while (my $seq = $sio->next_seq()) {
  push @seqs,$seq;
}

# Run Minimo using input sequence objects and returning an assembly file
my $asm_file = 'results.ace';
$factory->out_type($asm_file);
$factory->run(\@seqs);

DESCRIPTION

Wrapper module for the local execution of the DNA assembly program Minimo.
Minimo is based on AMOS (http://sourceforge.net/apps/mediawiki/amos/) and
implements the same conservative assembly algorithm as Minimus
(http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus).

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 - Florent E Angly

Email: florent-dot-angly-at-gmail-dot-com

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : $assembler->new( -min_len   => 50,
                           -min_ident => 95 );
Function: Creates a Minimo factory
Returns : A Bio::Tools::Run::Minimo object
Args    : Minimo options available in this module:
    qual_in      Input quality score file
    good_qual    Quality score to set for bases within the clear
                   range if no quality file was given (default: 30)
    bad_qual     Quality score to set for bases outside clear range
                   if no quality file was given (default: 10). If your
                   sequences are trimmed, try the same value as GOOD_QUAL.
    min_len / minimum_overlap_length
                 Minimum contig overlap length (between 20 and 100 bp,
                   default: 35)
    min_ident / minimum_overlap_similarity
                 Minimum contig overlap identity percentage (between 0
                   and 100 %, default: 98)
    aln_wiggle   Alignment wiggle value when determining the consensus
                   sequence (default: 2 bp)
    out_prefix   Prefix to use for the output file path and name

out_type

Title   : out_type
Usage   : $factory->out_type('Bio::Assembly::ScaffoldI')
Function: Get/set the desired type of output
Returns : The type of results to return
Args    : Desired type of results to return (optional):
                'Bio::Assembly::IO' object
                'Bio::Assembly::ScaffoldI' object (default)
                The name of a file to save the results in

run

Title   :   run
Usage   :   $factory->run($fasta_file);
Function:   Run TIGR Assembler
Returns :   - a Bio::Assembly::ScaffoldI object, a Bio::Assembly::IO
              object, a filename, or undef if all sequences were too small to
              be usable
Returns :   Assembly results (file, IO object or assembly object)
Args    :   - sequence input (FASTA file or sequence object arrayref)
            - optional quality score input (QUAL file or quality score object
              arrayref)

_run

Title   :   _run
Usage   :   $factory->_run()
Function:   Make a system call and run TIGR Assembler
Returns :   An assembly file
Args    :   - FASTA file
            - optional QUAL file

_clean_file

Title   :   _clean_file
Usage   :   $factory->_clean_file($file)
Function:   Clean file in place by removing NULL characters. NULL characters
            can be present in the output files of AMOS 2.0.8 but they do not
            validate as proper sequence characters in Bioperl.
Returns :   1 for success
Args    :   Filename