- AUTHOR - Robson Francisco de Souza
- Parser methods
Bio::Assembly::IO::ace - module to load ACE files from various assembly programs
# 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 = $io->next_assembly;
This package loads the standard ACE files generated by various assembly programs (Phrap, CAP3, Newbler, Arachne, ...). It was written to be used as a driver module for Bio::Assembly::IO input/output.
Assemblies are loaded into Bio::Assembly::Scaffold objects composed by Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Only the ACE file is used, so if you need singlets, make sure that they are present in the ACE file.
A description of the ACE format is available at http://www.cbcb.umd.edu/research/contig_representation.shtml#ACE
In addition to default "_aligned_coord:$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.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_assembly Usage : $unigene = $stream->next_assembly() Function: returns the next assembly in the stream Returns : Bio::Assembly::Scaffold object Args : NONE
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