NAME

Bio::Assembly::IO::ace - module to load phrap ACE files.

SYNOPSIS

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

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

    $assembly = $io->next_assembly;

DESCRIPTION

This package loads the ACE files from the (phred/phrap/consed) package by Phill Green. 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 objects. 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

"_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 phrap 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

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 Phrap compatible ACE format
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold object