Provided by: libbio-perl-perl_1.6.923-1_all 
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://redmine.open-bio.org/projects/bioperl/
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 :