Bio::Assembly::IO::ace(3pm) | User Contributed Perl Documentation | Bio::Assembly::IO::ace(3pm) |
Bio::Assembly::IO::ace - module to load ACE files from various assembly programs
# 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 $in_io = Bio::Assembly::IO->new( -file => 'results.ace', -format => 'ace', -variant => '454' );
This package loads the standard ACE files generated by various assembly programs (Phrap, CAP3, Newbler, Arachne, ...). It was written to be used as a driver module for Bio::Assembly::IO input/output.
Assemblies are loaded into Bio::Assembly::Scaffold objects composed by Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Only the ACE file is used, so if you need singlets, make sure that they are present in the ACE file.
A brief description of the ACE format is available at http://www.cbcb.umd.edu/research/contig_representation.shtml#ACE Read the full format description from http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt
In addition to default "_aligned_coord:$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.
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 '-'.
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
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.
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
Email rfsouza@citri.iq.usp.br
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_assembly Usage : $scaffold = $stream->next_assembly() Function: returns the next assembly in the stream Returns : a Bio::Assembly::Scaffold object Args : none
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
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
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
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
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)
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'
Title : _write_read Usage : $ass_io->_write_read($read, $contig) Function: Write a read object in ACE compatible format Returns : 1 on success, 0 for error Args : a Bio::LocatableSeq read the Contig or Singlet object that this read belongs to
Title : _formatted_seq Usage : Bio::Assembly::IO::ace::_formatted_seq($sequence, $line_width) Function: Format a sequence for ACE output: i ) replace gaps in the sequence by the '*' char ii) split the sequence on multiple lines as needed Returns : new sequence string Args : sequence string on one line maximum line width
Title : _formatted_qual Usage : Bio::Assembly::IO::ace::_formatted_qual($qual_arr, $sequence, $line_width, $qual_default) Function: Format quality scores for ACE output: i ) use the default quality values when they are missing ii ) remove gaps (they get no score in ACE) iii) split the quality scores on several lines as needed Returns : new quality score string Args : quality score array reference corresponding sequence string maximum line width default quality score
Title : _input_qual Usage : Bio::Assembly::IO::ace::_input_qual($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
Title : _initialize Usage : $ass_io->_initialize(@args) Function: Initialize the Bio::Assembly::IO object with the proper ACE variant Returns : Args :
2018-10-27 | perl v5.26.2 |