= Incompatible and important changes since the BioRuby 0.6.4 release A lot of changes have been made to the BioRuby after the version 0.6.4 is released. --- Ruby 1.6 series are no longer supported. We use autoload functionality and many other libraries bundled in Ruby 1.8.2 (such as SOAP, open-uri, pp etc.) by default. --- BioRuby will be loaded about 30 times faster than before. As we changed to use autoload instead of require, time required to start up the BioRuby library made surprisingly faster. Other changes (including exciting BioRuby shell etc.) made in this release is described in this file. == New features --- BioRuby shell Command line user interface for the BioRuby is included. You can invoke the shell by % bioruby --- UnitTest Test::Unit now covers wide range of the BioRuby library. You can run them by % ruby test/runner.rb or % ruby install.rb config % ruby install.rb setup % ruby install.rb test during the installation procedure. --- Documents README, README.DEV, doc/Tutorial.rd, doc/Tutorial.rd.ja etc. are updated or newly added. == Incompatible changes --- Bio::Sequence * Bio::Sequence::NA#gc_percent returns integer instead of float * Bio::Sequence::NA#gc (was aliased to gc_percent) is removed Previously, GC% is rounded to one decimal place. However, how many digits should be left when rounding the value is not clear and as the GC% is an rough measure by its nature, we have changed to return integer part only. If you need a precise value, you can calculate it by values from the 'composition' method by your own criteria. Also, the 'gc' method is removed as the method name doesn't represent its value is ambiguous. * Bio::Sequence#blast * Bio::Sequence#fasta These two methods are removed. Use Bio::Blast and Bio::Fasta to execute BLAST and FASTA search. --- Bio::NucleicAcid Bio::NucleicAcid::Names and Bio::NucleicAcid::Weight no longer exists. Bio::NucleicAcid::Names is renamed to Bio::NucleicAcid::Data::NAMES and can be accessed by Bio::NucleicAcid#names, Bio::NucleicAcid.names methods and Bio::NucleicAcid::WEIGHT hash as the Data module is included. Bio::NucleicAcid::Weight is renamed to Bio::NucleicAcid::Data::Weight and can be accessed by Bio::NucleicAcid#weight, Bio::NucleicAcid.weight methods and Bio::NucleicAcid::WEIGHT hash as the Data module is included. --- Bio::AminoAcid Bio::AminoAcid::Names and Bio::AminoAcid::Weight no longer exists. Bio::AminoAcid::Names is renamed to Bio::AminoAcid::Data::NAMES and can be accessed by Bio::AminoAcid#names, Bio::AminoAcid.names methods and Bio::AminoAcid::WEIGHT hash as the Data module is included. Bio::AminoAcid::Weight is renamed to Bio::AminoAcid::Data::Weight and can be accessed by Bio::AminoAcid#weight, Bio::AminoAcid.weight methods and Bio::AminoAcid::WEIGHT hash as the Data module is included. --- Bio::CodonTable Bio::CodonTable::Tables, Bio::CodonTable::Definitions, Bio::CodonTable::Starts, and Bio::CodonTable::Stops are renamed to Bio::CodonTable::TABLES, Bio::CodonTable::DEFINITIONS, Bio::CodonTable::STARTS, and Bio::CodonTable::STOPS respectively. --- Bio::KEGG::Microarrays, Bio::KEGG::Microarray * lib/bio/db/kegg/microarray.rb is renamed to lib/bio/db/kegg/expression.rb * Bio::KEGG::Microarray is renamed to Bio::KEGG::EXPRESSION * Bio::KEGG::Microarrays is removed Bio::KEGG::Microarrays was intended to store a series of microarray expressions as a Hash of Array -like data structure, gene1 => [exp1, exp2, exp3, ... ] gene2 => [exp1, exp2, exp3, ... ] however, it is not utilized well and more suitable container class can be proposed. Until then, this class is removed. # # Following changes are suspended for a while (not yet introduced for now) # # --- Bio::Pathway # # * Bio::Pathway#nodes returns an Array of the node objects instead of # the number of the node objects. # * Bio::Pathway#edges returns an Array of the edge objects instead of # the number of the edge objects. # --- Bio::GenBank Bio::GenBank#gc is removed as the value can be calculated by the Bio::Sequence::NA#gc method and the method is also changed to return integer instead of float. Bio::GenBank#varnacular_name is renamed to Bio::GenBank#vernacular_name as it was a typo. --- Bio::GenBank::Common * lib/bio/db/genbank/common.rb is removed. Renamed to Bio::NCBIDB::Common for the simple autoload dependency. --- Bio::EMBL::Common * lib/bio/db/embl/common.rb is removed. Renamed to Bio::EMBLDB::Common for the simple autoload dependency. --- Bio::KEGG::GENES * lib/bio/db/kegg/genes.rb linkdb method is changed to return a Hash of an Array of entry IDs instead of a Hash of a entry ID string. --- Bio::TRANSFAC * Bio::TFMATRIX is renamed to Bio::TRANSFAC::MATRIX * Bio::TFSITE is renamed to Bio::TRANSFAC::SITE * Bio::TFFACTOR is renamed to Bio::TRANSFAC::FACTOR * Bio::TFCELL is renamed to Bio::TRANSFAC::CELL * Bio::TFCLASS is renamed to Bio::TRANSFAC::CLASS * Bio::TFGENE is renamed to Bio::TRANSFAC::GENE --- Bio::GFF * Bio::GFF2 is renamed to Bio::GFF::GFF2 * Bio::GFF3 is renamed to Bio::GFF::GFF3 --- Bio::Alignment * Old Bio::Alignment class is renamed to Bio::Alignment::OriginalAlignment. Now, new Bio::Alignment is a module. However, you don't mind so much because most of the class methods previously existed are defined to delegate to the new Bio::Alignment::OriginalAlignment class, for keeping backward compatibility. * New classes and modules are introduced. Please refer RDoc. * each_site and some methods changed to return Bio::Alignment::Site, which inherits Array (previously returned Array). * consensus_iupac now returns only standard bases 'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v', 'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or '?' (or missing_char, in EnumerableExtension#consensus_iupac). Note that consensus_iupac now does not return u and invalid letters not defined in IUPAC standard even if all bases are equal. * There are more and more changes to be written... --- Bio::PDB * Bio::PDB::Atom is removed. Instead, please use Bio::PDB::Record::ATOM and Bio::PDB::Record::HETATM. * Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely changed. Now, Record is changed from hash to Struct, and method_missing is no longer used. * In the "MODEL" record, model_serial is changed to serial. * In records, record_type is changed to record_name. * In any records, record_type is changed to record_name. * In most records contains real numbers, changed to return float values instead of strings. * Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation, Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List, Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list, Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under Bio::PDB::DataType. * There are more and more changes to be written... === Deleted files : lib/bio/db/genbank.rb : lib/bio/db/embl.rb These files are removed as we changed to use autoload. You can safely replace require 'bio/db/genbank' or require 'bio/db/embl' in your code to require 'bio' and this change will also speeds up loading time if you only need one of the sub classes under the genbank/ or embl/ directory. : lib/bio/extend.rb This file contained some additional methods to String and Array classes. The methods added to Array are already included in Ruby itself since the version 1.8, and the methods added to String are moved to the BioRuby shell (lib/bio/shell/plugin/seq.rb).