Rechercher une page de manuel
Bio::Tools::Run::TigrAssembler.3pm
Langue: en
Version: 2009-11-04 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::TigrAssembler - Wrapper for local execution of TIGR Assemblerv2.0
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]
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre