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

NAME

       Bio::Tools::Run::TigrAssembler - Wrapper for local execution of TIGR Assembler
	v2

SYNOPSIS

	 use Bio::Tools::Run::TigrAssembler;
	 # Run TIGR Assembler using an input FASTA file
	 my $factory = Bio::Tools::Run::TigrAssembler->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 TIGR Assembler with input sequence objects and return an assembly file
	 my $asm_file = 'results.tigr';
	 $factory->out_type($asm_file);
	 $factory->run(@seqs);

	 # Use LIGR Assembler instead
	 my $ligr = Bio::Tools::Run::TigrAssembler->new(
	   -program_name => 'LIGR_Assembler',
	   -trimmed_seq  => 1
	 );
	 $ligr->run(@seqs);

DESCRIPTION

	 Wrapper module for the local execution of the DNA assembly program TIGR
	 Assembler v2.0. TIGR Assembler is open source software under The Artistic
	 License and available at: http://www.tigr.org/software/assembler/

	 This module runs TIGR Assembler by feeding it a FASTA file or sequence objects
	 and returning an assembly file or assembly and IO objects. When the input is
	 Bioperl object, sequences less than 39 bp long are filtered out since they are
	 not supported by TIGR Assembler.

	 If provided in the following way, TIGR Assembler will use additional
	 information present in the sequence descriptions for assembly:
	   >seq_name minimum_clone_length maximum_clone_length median_clone_length
	    clear_end5 clear_end3
	   or
	   >db|seq_name minimum_clone_length maximum_clone_length median_clone_length
	    clear_end5 clear_end3
	   e.g.
	   >GHIBF57F 500 3000 1750 33 587

	 This module also supports LIGR Assembler, a variant of TIGR Assembler:
	   http://sourceforge.net/projects/ligr-assembler/

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	: $factory->new( -minimum_percent  => 95,
				 -minimum_length   => 50,
				 -include_singlets => 1  );
	Function: Create a TIGR Assembler factory
	Returns : A Bio::Tools::Run::TigrAssembler object
	Args	:

       TIGR Assembler options available in this module:

	 minimum_percent / minimum_overlap_similarity: the minimum percent identity
	   that two DNA fragments must achieve over their entire region of overlap in
	   order to be considered as a possible assembly. Adjustments are made by the
	   program to take into account that the ends of sequences are lower quality
	   and doubled base calls are the most frequent sequencing error.
	 minimum_length / minimum_overlap_length: the minimum length two DNA fragments
	   must overlap to be considered as a possible assembly (warning: this option
	   is not strictly respected by TIGR Assembler...)
	 include_singlets: a flag which indicates that singletons (assemblies made up
	   of a single DNA fragment) should be included in the lassie output_file - the
	   default is to not include singletons.
	 max_err_32: the maximum number + 1 of alignment errors (mismatches or gaps)
	   allowed within any contiguous 32 base pairs in the overlap region between
	   two DNA fragments in the same assembly. This is meant to split apart splice
	   variants which have short splice differences and would not be disqualified
	   by the -p minimum_percent parameter.
	 consider_low_scores: a flag which causes even very LOW pairwise scores to be
	   considered - caution using this flag may cause longer run time and a worse
	   assembly.
	 maximum_end: the maximum length at the end of a DNA fragment that does not
	   match another overlapping DNA fragment (sometimes referred to as overhang)
	   that will not disqualify a DNA fragment from becoming part of an assembly.
	 ignore_tandem_32mers: a flag which causes tandem 32mers (a tandem 32mer is a
	   32mer which occurs more than once in at least one sequence read) to be
	   ignored (this is now the default behavior and this flag is for backward
	   compatibility)
	 use_tandem_32mers: a flag which causes tandem 32mers to be used for pairwise
	   comparison opposite of the -t flag which is now the default).
	 safe_merging_stop: a flag which causes merging to stop when only sequences
	   which appear to be repeats are left and these cannot be merged based on
	   clone length constraints.
	 not_random: a flag which indicates that the DNA fragments in the input_file
	   should not be treated as random genomic fragments for the purpose of
	   determining repeat regions.
	 resort_after: specifies how many sequences should be merged before resorting
	   the possible merges based on clone constraints.

       LIGR Assembler has the same options as TIGR Assembler, and the following:

	 incl_bad_seq: keep all sequences including potential chimeras and splice variants
	 trimmed_seq: indicates that the sequences are trimmed. High quality scores will be
	   given on the whole sequence length instead of just in the middle)

   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	:   $assembler->_run()
	Function:   Make a system call and run Newbler
	Returns :   An assembly file
	Args	:   - FASTA file, SFF file and MID, or analysis dir and MID
		    - optional QUAL file

   _remove_small_sequences
	Title	:   _remove_small_sequences
	Usage	:   $assembler->_remove_small_sequences(@seqs, @quals)
	Function:   Remove sequences below a threshold length
	Returns :   a new sequence object array reference
		    a new quality score object array reference
	Args	:   sequence object array reference
		    quality score object array reference (optional)

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