ngoto-bio 1.2.9.9001

data/doc/Changes-0.7.rd

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+= 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 standard (bundled) libraries
+(such as SOAP, open-uri, pp etc.) only in Ruby >1.8.2.
+
+--- 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 newly introduced BioRuby shell etc.) made
+in this series will be described in this file.
+
+== New features
+
+--- BioRuby shell
+
+A new command line user interface for the BioRuby is now 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 is completely refactored to be a container class for
+any sequence annotations.  Functionalities are separated into several
+files under the lib/bio/sequence/ directory as
+
+  * common.rb : module provides common methods for NA and AA sequences
+  * compat.rb : methods for backward compatibility
+  * aa.rb     : Bio::Sequence::AA class
+  * na.rb     : Bio::Sequence::NA class
+  * format.rb : module for format conversion
+
+Bio::Sequence is no longer a sub-class of String, instead,
+Bio::Sequence::NA and AA inherits String directly.
+
+* 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 to make simplify the autoload dependency.
+
+--- Bio::EMBL::Common
+
+* lib/bio/db/embl/common.rb is removed.
+
+Renamed to Bio::EMBLDB::Common to make simplify the 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
+
+In 0.7.0:
+
+* 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...
+
+In 1.1.0:
+
+* Bio::Alignment::ClustalWFormatter is removed and methods in this module
+  are renemed and moved to Bio::Alignment::Output.
+
+--- Bio::PDB
+
+In 0.7.0:
+
+* 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, records is changed from hash to Struct objects.
+  (Note that method_missing is no longer used.)
+* In records, "do_parse" is now automatically called.
+  Users don't need to call do_parse explicitly.
+  (0.7.0 feature: "inspect" does not call do_parse.)
+  (0.7.1 feature: "inspect" calls do_parse.)
+* In the "MODEL" record, model_serial is changed to serial.
+* In records, record_type is changed to record_name.
+* In most records contains real numbers, return values are changed
+  to float instead of string.
+* 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...
+
+In 0.7.1:
+
+* Heterogens and HETATMs are completely separeted from residues and ATOMs.
+  HETATMs (Bio::PDB::Record::HETATM objects) are stored in
+  Bio::PDB::Heterogen (which inherits Bio::PDB::Residue).
+* Waters (resName=="HOH") are treated as normal heterogens.
+  Model#solvents is still available but it will be deprecated.
+* In Bio::PDB::Chain, adding "LIGAND" to the heterogen id is no longer
+  available. Instead, please use Chain#get_heterogen_by_id method.
+  In addition, Bio::{PDB|PDB::Model::PDB::Chain}#heterogens, #each_heterogen,
+  #find_heterogen, Bio::{PDB|PDB::Model::PDB::Chain::PDB::Heterogen}#hetatms,
+  #each_hetatm, #find_hetatm methods are added.
+* Bio::PDB#seqres returns Bio::Sequence::NA object if the chain seems to be
+  a nucleic acid sequence.
+* There are more and more changes to be written...
+
+In 1.1.0:
+
+* In Bio::PDB::ATOM#name, #resName, #iCode, and #charge, whitespaces are
+  stripped during initializing.
+* In Bio::PDB::ATOM#segID, whitespaces are right-stripped during initializing.
+* In Bio::PDB::ATOM#element, whitespaces are left-stripped during initializing.
+* Bio::PDB::HETATM#name, #resName, #iCode, #charge, #segID, and #element
+  are also subject to the above changes, because Bio::PDB::HETATM inherits
+  Bio::PDB::ATOM.
+* Bio::PDB::Residue#[] and Bio::PDB::Heterogen#[] are changed to use the
+  name field for selecting atoms, because the element field is not useful
+  for selecting atoms and is not used in many pdb files.
+* Bio::PDB#record is changed to return an empty array instead of nil
+  for a nonexistent record.
+
+--- Bio::FlatFile
+
+In 0.7.2:
+
+* Bio::FlatFile.open, Bio::FlatFile.auto and Bio::FlatFile.new are changed
+  not to accept the last argument to specify raw mode, e.g. :raw => true,
+  :raw => false, true or false. Instead, please use Bio::FlatFile#raw=
+  method after creating a new object.
+* Now, first argument of Bio::FlatFile.open, which shall be a database
+  class or nil, can be omitted, and you can do
+  Bio::FlatFile.open(filename, ...). Note that 
+  Bio::FlatFile.open(dbclass, filaname, ...) is still available.
+* Bio::FlatFile#io is obsoleted. Please use Bio::FlatFile#to_io instead.
+* When reading GenBank or GenPept files, comments at the  head of the file
+  before the first "LOCUS" lines are now skipped by default.
+  When reading other file formats, white space characters are skipped.
+* File format autodetection routine is completely rewritten.
+  If it fails to determine data format which was previously determined,
+  please report us with the data.
+* Internal structure is now completely changed. Codes depend on the internal
+  structure (which is not recommended) would not work.
+
+In 1.1.0:
+
+* Bio::FlatFile#entry_start_pos and #entry_ended_pos are enabled
+  only when Bio::FlatFile#entry_pos_flag is true.
+
+--- Bio::ClustalW, Bio::MAFFT, Bio::Sim4
+
+In 1.1.0:
+
+* Bio::(ClustalW|MAFFT|Sim4)#option is changed to #options.
+* Bio::ClustalW::errorlog and Bio::(MAFFT|Sim4)#log are removed.
+  No replacements/alternatives are available.
+
+--- Bio::ClustalW, Bio::MAFFT
+
+In 1.1.0:
+
+* Bio::(ClustalW|MAFFT)#query_align, #query_string, #query_by_filename
+  are changed not to get second (and third, ...) arguments.
+* Bio::(ClustalW|MAFFT)#query, #query_string, #query_by_filename
+  are changed not trying to guess whether given data is nucleotide or protein.
+* Return value of Bio::(ClustalW|MAFFT)#query with no arguments is changed.
+  If the program exists normally (exit status is 0), returns true.
+  Otherwise, returns false.
+
+--- Bio::MAFFT
+
+In 1.1.0:
+
+* Bio::MAFFT#output is changed to return a string of multi-fasta
+  formmatted text instead of Array of Bio::FastaFormat objects.
+  To get an array of Bio::FastaFormat objects, please use
+  report.data instead.
+
+--- Bio::MAFFT::Report
+
+In 1.1.0:
+
+* Bio::MAFFT::Report#initialize is changed to get a string of multi-fasta
+  formmatted text instead of Array.
+
+--- Bio::BLAST::Default::Report, Bio::BLAST::Default::Report::Hit,
+    Bio::BLAST::Default::Report::HSP, Bio::BLAST::WU::Report,
+    Bio::BLAST::WU::Report::Hit, Bio::BLAST::WU::Report::HSP
+
+In 1.1.0:
+
+* Hit#evalue, HSP#evalue, WU::Hit#pvalue, and WU::HSP#pvalue are
+  changed to return a Float object instead of a String object.
+* Report#expect, Hit#bit_score, and HSP#bit_score are changed to return
+  a Float object or nil instead of a String object or nil.
+* Following methods are changed to return an integer value or nil
+  instead of a string or nil: score, percent_identity, percent_positive,
+  percent_gaps.
+
+=== 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 even 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).
+
+

data/doc/Changes-1.3.rdoc

@@ -0,0 +1,195 @@
+= Incompatible and important changes since the BioRuby 1.2.1 release
+
+A lot of changes have been made to the BioRuby after the version 1.2.1
+is released.
+
+== New features
+
+=== Support for sequence output with improvements of Bio::Sequence
+
+The outputting of EMBL and GenBank formatted text are now supported in the
+Bio::Sequence class. See the document of Bio::Sequence#output for details.
+You can also create Bio::Sequence objects from many kinds of data such as
+Bio::GenBank, Bio::EMBL, and Bio::FastaFormat by using the to_biosequence
+method.
+
+=== BioSQL support
+
+BioSQL support is completely rewritten by using ActiveRecord.
+
+=== Bio::Blast
+
+Bio::Blast#reports can parse NCBI default (-m 0) format and tabular (-m 8)
+format, in addition to XML (-m 7) format.
+
+Bio::Blast::Report now supports XML format with multiple query sequences
+generated by blastall 2.2.14 or later.
+
+Bio::Blast.remote supports DDBJ, in addition to GenomeNet.
+In addition, a list of available blast databases on remote sites
+can be obtained by using Bio::Blast::Remote::DDBJ.databases and
+Bio::Blast::Remote::GenomeNet.databases methods. Note that the above
+remote blast methods may be changed in the future to support NCBI.
+
+Bio::Blast::RPSBlast::Report is newly added, a parser for NCBI RPS Blast
+(Reversed Position Specific Blast) default (-m 0 option) results.
+
+=== Bio::GFF::GFF2 and Bio::GFF::GFF3
+
+The outputting of GFF2/GFF3-formatted text is now supported. However, many
+incompatible changes have been made (See below for details).
+
+=== Bio::Hinv
+
+H-Invitational Database web service (REST) client class is newly added.
+
+=== Bio::NCBI::REST
+
+NCBI E-Utilities client class is newly added.
+
+=== Bio::PAML::Codeml and Bio::PAML::Codeml::Report
+
+Bio::PAML::Codeml, wrapper for PAML codeml program, and
+Bio::PAML::Codeml::Report, parser for codeml result are newly added,
+though some of them are still under construction and too specific to
+particular use cases.
+
+=== Bio::Locations
+
+New method Bio::Locations#to_s is added to support output of features.
+
+== Deprecated classes
+
+=== Bio::Features
+
+Bio::Features is obsoleted and changed to an array of Bio::Feature object
+with some backward compatibility methods.  The backward compatibility methods
+will soon be removed in the future.
+
+=== Bio::References
+
+Bio::References is obsoleted and changed to an array of Bio::Reference object
+with some backward compatibility methods.  The backward compatibility methods
+will soon be removed in the future.
+
+== Incompatible changes
+
+=== Bio::Sequence
+
+Bio::Sequence#date is removed.  Alternatively, date_created or date_modified
+can be used.
+
+Bio::Sequence#taxonomy is changed to be an alias of classification, and
+the data type is changed to an array of string.
+
+=== Bio::Locations and Bio::Location
+
+A carat in a location (e.g. "123^124") is now parsed, instead of being
+replaced by "..".  To distinguish from normal "..", a new attribute
+Bio::Location#carat is used.
+
+"order(...)" or "group(...)" are also parsed, instead of being regarded
+as "join(...)".  To distinguish from "join(...)", a new attribute
+Bio::Locations#operator is used.  When "order(...)" or "group(...)",
+the attribute is set to :order or :group, respectively.  Note that
+"group(...)" is already deprecated in EMBL/GenBank/DDBJ.
+
+=== Bio::Blast::Default::Report and Bio::Blast::WU::Report
+
+Iteration#lambda, #kappa, #entropy, #gapped_lambda, #gapped_kappa,
+and #gapped_entropy, and the same methods in the Report class are
+changed to return float or nil instead of string or nil.
+
+=== Bio::Blat
+
+When reading BLAT psl (or pslx) data by using Bio::FlatFile, it checks
+each query name and returns a new entry object when the query name is
+changed from previous queries. This is, data is stored to two or more
+Bio::Blat::Report objects, instead of previous version's behavior
+(always reads all data at once and stores to a Bio::Blat::Report object).
+
+=== Bio::GFF, Bio::GFF::GFF2 and Bio::GFF::GFF3
+
+Bio::GFF::Record#comments is renamed to #comment, and #comments= is
+renamed to #comment=, because they only allow a single String (or nil)
+and the plural form "comments" may be confusable.  The "comments" and
+"comments=" methods can still be used, but warning messages will be
+shown when using in GFF2::Record and GFF3::Record objects.
+
+See below about GFF2 and/or GFF3 specific changes.
+
+=== Bio::GFF::GFF2 and Bio::GFF::GFF3
+
+Bio::GFF::GFF2::Record.new and Bio::GFF::GFF3::Record.new can also
+get 9 arguments corresponding to GFF columns, which helps to create
+Record object directly without formatted text.
+
+Bio::GFF::GFF2::Record#start, #end, and #frame return Integer or nil,
+and #score returns Float or nil, instead of String or nil.
+The same changes are also made to Bio::GFF::GFF3::Record.
+
+Bio::GFF::GFF2::Record#attributes and Bio::GFF::GFF3::Record#attributes
+are changed to return a nested Array, containing [ tag, value ] pairs,
+because of supporting multiple tags in the same tag names.  If you want
+to get a Hash, use Record#attributes_to_hash method, though some
+tag-value pairs in the same tag names may be lost.  Note that
+Bio::GFF::Record#attribute still returns a Hash for compatibility.
+
+New methods for getting, setting and manipulating attributes are added
+to Bio::GFF::GFF2::Record and Bio::GFF::GFF3::Record classes:
+attribute, get_attribute, get_attributes, set_attribute, replace_attributes,
+add_attribute, delete_attribute, delete_attributes, sort_attributes_by_tag!.
+It is recommended to use these methods instead of directly manipulating
+the array returned by Record#attributes.
+
+Bio::GFF::GFF2#to_s, Bio::GFF::GFF3#to_s, Bio::GFF::GFF2::Record#to_s,
+and Bio::GFF::GFF3::Record#to_s are added to support output of
+GFF2/GFF3 data.
+
+=== Bio::GFF::GFF2
+
+GFF2 attribute values are now automatically unescaped.  In addition,
+if a value of an attribute is consisted of two or more tokens delimited
+by spaces, an object of the new class Bio::GFF::GFF2::Record::Value is
+returned instead of String.  The new class Bio::GFF::GFF2::Record::Value
+aims to store a parsed value of an attribute.  If you really want to get
+unparsed string, Bio::GFF::GFF2::Record::Value#to_s can be used.
+
+The metadata (lines beginning with "##") are parsed to
+Bio::GFF::GFF2::MetaData objects and are stored to Bio::GFF::GFF2#metadata
+as an array, except the "##gff-version" line.  The "##gff-version" version
+string is stored to the Bio::GFF::GFF2#gff_version as a string.
+
+=== Bio::GFF::GFF3
+
+Aliases of columns which are renamed in the GFF3 specification are added
+to the Bio::GFF::GFF3::Record class: seqid (column 1; alias of "seqname"),
+feature_type (column 3; alias of "feature"; in the GFF3 spec, it is
+called "type", but because "type" is already used by Ruby, we use
+"feature_type"), phase (column 8; formerly "frame"). Original names can
+still be used because they are only aliases.
+
+Sequences bundled within GFF3 after "##FASTA" are now supported
+(Bio::GFF::GFF3#sequences).
+
+GFF3 attribute keys and values are automatically unescaped. Each attribute
+value is stored as a string, except for special attributes listed below:
+* Bio::GFF::GFF3::Record::Target to store a "Target" attribute.
+* Bio::GFF::GFF3::Record::Gap to store a "Gap" attribute.
+
+The metadata (lines beginning with "##") are parsed to
+Bio::GFF::GFF3::MetaData objects and stored to Bio::GFF::GFF3#metadata
+as an array, except "##gff-version", "##sequence-region", "###",
+and "##FASTA" lines.
+* "##gff-version" version string is stored to Bio::GFF::GFF3#gff_version.
+* "##sequence-region" lines are parsed to Bio::GFF::GFF3::SequenceRegion
+  objects and stored to Bio::GFF::GFF3#sequence_regions as an array.
+* "###" lines are parsed to Bio::GFF::GFF3::RecordBoundary objects.
+* "##FASTA" is regarded as the beginning of bundled sequences.
+
+=== Bio::SQL and BioSQL related classes
+
+BioSQL support is completely rewritten by using ActiveRecord. See documents
+in lib/bio/io/sql.rb, lib/bio/io/biosql, and lib/bio/db/biosql for details
+of changes and usage of the classes/modules.
+