Bio::Tools::Run::Minimo(3) 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. 

  [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:

[email protected]

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

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