/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ 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;

# 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)
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    :