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BioPerl-1.6.1
River stage two • 60 direct dependents • 65 total dependents
33 ++
/ Bio::Assembly::IO::ace

NAME

Bio::Assembly::IO::ace - module to load ACE files from various assembly programs

SYNOPSIS

    # Building an input stream
    use Bio::Assembly::IO;

    # Assembly loading methods
    $io = Bio::Assembly::IO->new( -file=>"SGC0-424.fasta.screen.ace.1",
                                  -format=>"ace" );

    $assembly = $io->next_assembly;

DESCRIPTION

This package loads the standard ACE files generated by various assembly programs (Phrap, CAP3, Newbler, Arachne, ...). It was written to be used as a driver module for Bio::Assembly::IO input/output.

Implemention

Assemblies are loaded into Bio::Assembly::Scaffold objects composed by Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Only the ACE file is used, so if you need singlets, make sure that they are present in the ACE file.

A description of the ACE format is available at http://www.cbcb.umd.edu/research/contig_representation.shtml#ACE

In addition to default "_aligned_coord:$seqID" feature class from Bio::Assembly::Contig, contig objects loaded by this module will have the following special feature classes in their feature collection:

"_align_clipping:$seqID" : location of subsequence in sequence $seqID which is aligned to the contig. If no feature containing this tag is present the read is considered low quality by consed

"_quality_clipping:$seqID" : location of good quality subsequence for sequence $seqID

"consensus tags", as they are called in Consed's documentation, is equivalent to a bioperl sequence feature and, therefore, are added to the feature collection using their type field (see Consed's README.txt file) as primary tag.

"read tags" are also sequence features and are stored as sub_SeqFeatures of the sequence's coordinate feature (the corresponding "_aligned_coord:$seqID" feature, easily accessed through get_seq_coord() method).

"whole assembly tags" have no start and end, as they are not associated to any particular sequence in the assembly, and are added to the assembly's annotation collection using "whole assembly" as tag.

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 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 - Robson Francisco de Souza

Email rfsouza@citri.iq.usp.br

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Parser methods

next_assembly

 Title   : next_assembly
 Usage   : $unigene = $stream->next_assembly()
 Function: returns the next assembly in the stream
 Returns : Bio::Assembly::Scaffold object
 Args    : NONE

write_assembly

    Title   : write_assembly
    Usage   : $ass_io->write_assembly($assembly)
    Function: Write the assembly object in ACE compatible format
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold object