Bio::Tools::Run::TigrAssembler.3pm

Langue: en

Autres versions - même langue

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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]