Bio::Tools::Run::Minimo(3pm)				User Contributed Perl Documentation			      Bio::Tools::Run::Minimo(3pm)

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

perl v5.12.3							    2011-06-18					      Bio::Tools::Run::Minimo(3pm)