Bio::Assembly::IO::ace(3)

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

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

    # Load a reference ACE assembly
    my $in_io = Bio::Assembly::IO->new( -file   => 'results.ace',
                                        -format => 'ace'          );

    # Read the entire scaffold
    my $scaffold = $in_io->next_assembly;

    # Or read one contig at a time to save resources
    while ( my $contig = $in_io->next_contig ) {
      # Do something ...
    }

    # Assembly writing methods
    my $out_io = Bio::Assembly::IO->new( -file   => ">output.ace",
                                         -format => 'ace' );
    $out_io->write_assembly( -scaffold => $scaffold,
                             -singlets => 1 );

    # Read the '454' Newbler variant of ACE instead of the default 'consed'
    # reference ACE variant
    my $in_io = Bio::Assembly::IO->new( -file   => 'results.ace',
                                        -format => 'ace-454'      );
    # or ...
    my $in_io = Bio::Assembly::IO->new( -file    => 'results.ace',
                                        -format  => 'ace',
                                        -variant => '454'      );

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 brief description of the ACE format is available at http://www.cbcb.umd.edu/research/contig_representation.shtml#ACE Read the full format description from http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt

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" (AF)
    Location of subsequence in read $seqID which is aligned to the contig. The
    coordinates are relative to the contig. If no feature containing this tag is
    present the read is considered low quality by Consed.

"_quality_clipping:$seqID" (AF)
    The location of high quality subsequence in read $seqID (relative to contig)

"_base_segments" (BS)
    Location of read subsequences used to build the consensus

"_read_tags:$readID" (RT)
    Sequence features stored as sub_SeqFeatures of the sequence's coordinate
    feature (the corresponding "_aligned_coord:$seqID" feature, easily accessed
    through get_seq_coord() method).

"_read_desc:$readID" (DS)
    Sequence features stored as sub_SeqFeatures of the read's coordinate feature

"consensus tags" (CT)
    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.

"whole assembly tags" (WA)
    They 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.

  Variants
The default ACE variant is called 'consed' and corresponds to the reference ACE format.

The ACE files produced by the 454 GS Assembler (Newbler) do not conform to the reference ACE format. In 454 ACE, the consensus sequence reported covers only its clear range and the start of the clear range consensus is defined as position 1. Consequently, aligned reads in the contig can have negative positions. Be sure to use the '454' variant to have positive alignment positions. No attempt is made to construct the missing part of the consensus sequence (beyond the clear range) based on the underlying reads in the contig. Instead the ends of the consensus are simply padded with the gap character '-'.

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:

  https://github.com/bioperl/bioperl-live/issues

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   : $scaffold = $stream->next_assembly()
 Function: returns the next assembly in the stream
 Returns : a Bio::Assembly::Scaffold object
 Args    : none

  next_contig
 Title   : next_contig
 Usage   : $scaffold = $stream->next_contig()
 Function: Returns the next contig or singlet in the ACE stream.
 Returns : a Bio::Assembly::Contig or Bio::Assembly::Single object
 Args    : none

  scaffold_annotations
 Title   : scaffold_annotations
 Usage   : $stream->scaffold_annotations($scaffold)
 Function: Add assembly and contig annotations to a scaffold. In the ACE format,
           annotations are the WA and CT tags.
 Returns : 1 for success
 Args    : a Bio::Assembly::Scaffold object to attach the annotations to

  write_assembly
    Title   : write_assembly
    Usage   : $ass_io->write_assembly($assembly)
    Function: Write the assembly object in ACE compatible format. The contig IDs
              are sorted naturally if the Sort::Naturally module is present, or
              lexically otherwise. Internally, write_assembly use the
              write_contig, write_footer and write_header methods. Use these
              methods if you want more control on the writing process.
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold object

  write_contig
    Title   : write_contig
    Usage   : $ass_io->write_contig($contig)
    Function: Write a contig or singlet object in ACE compatible format. Quality
              scores are automatically generated if the contig does not contain
              any
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Contig or Singlet object

  write_header
    Title   : write_header
    Usage   : $ass_io->write_header($scaffold)
                  or
              $ass_io->write_header(\@contigs);
                  or
              $ass_io->write_header();
    Function: Write ACE header (AS tags). You can call this function at any time,
              i.e. not necessarily at the start of the stream - this is useful
              if you have an undetermined number of contigs to write to ACE, e.g:
                for my $contig (@list_of_contigs) {
                  $ass_io->_write_contig($contig);
                }
                $ass_io->_write_header();
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold
                  or
              an arrayref of Bio::Assembly::Contig
                  or
              nothing (the header is dynamically written based on the ACE file
              content)

  write_footer
    Title   : write_footer
    Usage   : $ass_io->write_footer($scaffold)
    Function: Write ACE footer (WA and CT tags).
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold object (optional)

  variant
 Title   : variant
 Usage   : $variant = $ass_io->variant();
 Function: Get and set method for the assembly variant. This is important since
           not all assemblers respect the reference ACE format.
 Returns : string
 Args    : string: 'consed' (default) or '454'

  _write_read
    Title   : _write_read
    Usage   : $ass_io->_write_read($read, $contig)
    Function: Write a read object in ACE compatible format
    Returns : 1 on success, 0 for error
    Args    : a Bio::LocatableSeq read
              the Contig or Singlet object that this read belongs to

  _formatted_seq
    Title   : _formatted_seq
    Usage   : Bio::Assembly::IO::ace::_formatted_seq($sequence, $line_width)
    Function: Format a sequence for ACE output:
              i ) replace gaps in the sequence by the '*' char
              ii) split the sequence on multiple lines as needed
    Returns : new sequence string
    Args    : sequence string on one line
              maximum line width

  _formatted_qual
    Title   : _formatted_qual
    Usage   : Bio::Assembly::IO::ace::_formatted_qual($qual_arr, $sequence, $line_width, $qual_default)
    Function: Format quality scores for ACE output:
              i  ) use the default quality values when they are missing
              ii ) remove gaps (they get no score in ACE)
              iii) split the quality scores on several lines as needed
    Returns : new quality score string
    Args    : quality score array reference
              corresponding sequence string
              maximum line width
              default quality score

  _input_qual
    Title   : _input_qual
    Usage   : Bio::Assembly::IO::ace::_input_qual($qual_string, $sequence)
    Function: Reads input quality string and converts it to an array of quality
              scores. Gaps get a quality score equals to the average of the
              quality score of its neighbours.
    Returns : new quality score array
    Args    : quality score string
              corresponding sequence string

  _initialize
    Title   : _initialize
    Usage   : $ass_io->_initialize(@args)
    Function: Initialize the Bio::Assembly::IO object with the proper ACE variant
    Returns :
    Args    :