Provided by: libbio-perl-run-perl_1.6.9-1_all bug

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)