Bio::Assembly::IO::aceUser Contributed Perl DocumentaBio::Assembly::IO::ace(3)NAMEBio::Assembly::IO::ace - module to load ACE files from various assembly
programs
SYNOPSIS
# Building an input stream
use Bio::Assembly::IO;
# Assembly loading methods
$io = Bio::Assembly::IO->new( -file=>"SGC0-424.fasta.screen.ace.1",
-format=>"ace" );
$assembly = $io->next_assembly;
DESCRIPTION
This package loads the standard ACE files generated by various assembly
programs (Phrap, CAP3, Newbler, Arachne, ...). It was written to be
used as a driver module for Bio::Assembly::IO input/output.
Implemention
Assemblies are loaded into Bio::Assembly::Scaffold objects composed by
Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Only the ACE
file is used, so if you need singlets, make sure that they are present
in the ACE file.
A description of the ACE format is available at
http://www.cbcb.umd.edu/research/contig_representation.shtml#ACE
In addition to default "_aligned_coord:$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 $seqID
which is aligned to the contig. If no
feature
containing this tag is present the read is
considered low quality by consed
"_quality_clipping:$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 "whole assembly" 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
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:
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 ACE compatible format
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Scaffold object
perl v5.14.1 2011-07-22 Bio::Assembly::IO::ace(3)
