Bio::Tools::Run::TigrAssembler man page on Pidora

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Bio::Tools::Run::TigrAUserbContributed Perl DBio::Tools::Run::TigrAssembler(3)

NAME
       Bio::Tools::Run::TigrAssembler - Wrapper for local execution of TIGR
       Assembler
	v2.0

SYNOPSIS
	 use Bio::Tools::Run::TigrAssembler;
	 my $assembler = Bio::Tools::Run::TigrAssembler->new();

	 # Pass the factory a Bio::Seq object array reference
	 # Returns a Bio::Assembly::Scaffold object array reference
	 my $asms = $assembler->run(\@seqs);

	 for my $asm (@$asms) {
	   # do something with assembled sequences
	 }

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/

	 The description enables to runs TIGR Assembler by feeding it sequence objects
	 and returning assembly objects. The input could be an array of Bio::PrimarySeq
	 or maybe Bio::Seq::Quality, in which case, the quality scores will
	 automatically be used during assembly. Sequences less than 40 bp long are
	 filtered out since they are not supported by TIGR Assembler. The
	 amount of memory in your machine may prevent you to assemble large sequence
	 datasets, but this module offers a way to split your dataset in smaller
	 datasets to be assembled _independently_. An array of Bio::Assembly::Scaffold
	 objects is returned.

	 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

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 - 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 _

   program_name
	Title	: program_name
	Usage	: $assembler>program_name()
	Function: get/set the program name
	Returns:  string
	Args	: string

   program_dir
	Title	: program_dir
	Usage	: $assembler->program_dir()
	Function: get/set the program dir
	Returns:  string
	Args	: string

   max_nof_seqs
	Title	: max_nof_seqs
	Usage	: $assembler->max_nof_seqs()
	Function: get/set the maximum number number of sequences to assemble at once
	Returns:  string
	Args	: string

   new
	Title	: new
	Usage	: $assembler->new( -minimum_percent  => 95,
				   -minimum_length   => 50,
				   -include_singlets => 1);
	Function: Creates a TIGR Assembler factory
	Returns : Bio::Tools::Run::TigrAssembler object
	Args	: TIGR Assembler options available in this module:
	 minimum_percent: 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: the minimum length two DNA fragments must overlap to be
	   considered as a possible assembly.
	 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
	   compatability)
	 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 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.

   run
	Title	:   run
	Usage	:   $obj->run(\@seqs, \@quals);
	Function:   Runs TIGR Assembler
	Returns :   a Bio::Assembly::ScaffoldI object array reference, or undef if all
		    sequences were too small to be usable
	Args	:   - sequences as a Bio::PrimarySeqI or Bio::SeqI arrayref (e.g. can
		      be Bio::Seq::Quality for sequences and quality scores in a same
		      object)
		    - optional Bio::Seq::PrimaryQual arrayref of quality scores if
		      you have your scores in different objects from your sequences.
		      Must have same ID as sequences and same order

   _write_seq_file
	Title	:   _write_seq_file
	Usage	:   $assembler->_write_seq_file(\@seqs, \@quals)
	Function:   Write temporary FASTA and QUAL files on disk
	Returns :   name of FASTA file
		    name of QUAL file (undef if no quality scoress)
	Args	:   Bio::PrimarySeq object array reference
		    optional quality objects array reference

   _run
	Title	:   _run
	Usage	:   $assembler->_run()
	Function:   Assembly step
	Returns :   Bio::Assembly::Scaffold object
		    assembly file location
	Args	:   FASTA file location
		    QUAL file location [optional]

perl v5.14.1			  2011-07-21 Bio::Tools::Run::TigrAssembler(3)
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