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#Change Log

  • UPDATE (v.0.6.5) Support Zebrafish DanRer10 and DanRer11 references.
  • UPDATE (v.0.6.4) Support Ruby 2.4 by using Rails 4.2 and the MySql2 gem v0.4 at BioHackathon2017 http://20
  • BUG-FIX (v.0.6.3) Bio::Ucsc::File::TwoBit#find_by_interval fails in retrieving reference sequences including entire "N" blocks, e.g. "aaaNNttt".
  • BUG-FIX (v.0.6.2) NoMemoryError in Bio::Ucsc::File::Twobit.open. Now internally File.open is used instead of Kernel.open.
  • UPDATE (v.0.6.1) Support new human hg38 reference. Newer tables after this release will be supported in later varsions.
  • NEW (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use ActiveSupport::Deprecation.silenced = true. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies.
  • UPDATE (v0.6.0): Ruby UCSC API is now licensed under the MIT License. See also the LICENSE.txt file.
  • BUG-FIX (v 0.5.3): Support ActiveRecord/ActiveSupport version 3 only.
  • UPDATE (v 0.5.3): The Rat Rn5 database is supported.
  • UPDATE (v 0.5.3): Bug-fix and update to pass all specs on Ruby 2.0.0-p0.
  • BUG-FIX (v 0.5.2): Fix a Bio::Ucsc::File::Twobit#subseq error when a query region is all included by a masked (Ns) region
  • UPDATE (v.0.5.1): Mouse mm10 database is supported.
  • BUG-FIX (v.0.5.0): Connecting multiple databeses simultaneously now works well.
  • NEW (v0.5.0): Support automatic definitions of table association using the "all.joiner" schema file.
  • NEW (v0.5.0): Instances in classes of the genePred tables, which have txStart and txEnd columns, now have #exons, #introns and #cdses methods. These methods return arrays of Bio::GenomicInterval instances. The arrays are sorted using gene strands.
  • BUG-FIX (v0.5.0): Bio::Ucsc::File::TwoBit#inspect now returns only short summary of the object instead of dumping a whole-genome sequence. This fixes hung-up in the irb environment.
  • UPDATE (v0.4.0): now <TABLE>#find_by_interval accepts both "chr1:123-456" and Bio::GenomicInterval objects
  • BUG-FIX (v0.4.0): By using the safe_attribute gem, newest version of ActiveRecord is supported.
  • UPDATE (v0.4.0): Bio::Ucsc::Reference is moved to Bio::Ucsc::File::Twobit (backward compatibility is kept). Bio::Ucsc::File::Twobit.open and Bio::Ucsc::File::Twobit#subseq is are introduced.
  • UPDATE (v0.4.0): <DB_NAME>::DBConnection.connect is simplified by the new <DB_NAME>.connect class method (backward compatibility is kept). Server parameters can be defined by using a hash being an argument of the method.
  • UPDATE (v0.3.2): Genomic interval queries are implemented using ARel's relation objects instead of (named) scopes. Usage of the API is not changed.
  • BUG (v0.3.1): Does not work with ActiveRecord version 3.1.0. Data retrieval methods occur the error, "(Object doesn't support #inspect)". The author is working on this bug. So far, please use version 3.0 seriese. Gemfile for gem dependencies is updated. Thanks for bug reports from Diego F. Pereira.
  • BUG-FIX (v0.3.1): "func" fields in tables did not work. The bug was fixed.
  • BUG-FIX (v0.3.1): PredGene-type tables without the bin index did not work. The bug was fixed.
  • NEW (v0.3.0): Now genomic interval queries are expressed using the named scope "with_interval". 'Table#find_(all_)by_interval' is now deprecated. Sorry for an inconstant API. However, this change enable combination queries using genomic intervals and any fields.
  • NEW (v0.3.0): Bio::GenomicInterval#bin_all and Bio::GenomicInterval#bin return the bin index for the given interval.
  • NEW (v0.3.0): Supporting JRuby 1.6.3 or later. Appropiate Java heap size may have to be specified to invoke JRuby, especially when you use Bio::Ucsc::Reference. Try jruby -J-Xmx3g your_script.rb to keep 3G byte heap.
  • NEW (v0.2.1): New genome assemblies are supported: [chimp] PanTro3, [orangutan] PonAbe2, [rhesus] RheMac2, [marmoset] CalJac3, [rat] Rn4, [guinea pig] CavPor3, [rabbit] OryCun2, [cat] FelCat4, [panda] AilMel1, [Dog] CanFam2, [horse] EquCab2, [pig] SusScr2, [sheep] OviAri1, [cow] BosTau4, [elephant] LoxAfr3, [opossum] MonDom5, [platypus] OrnAna1, [chicken] GalGal3, [zebra finch] TaeGut1, [lizard] AnoCar2, [X. tropicalis] XenTro2, [zebrafish] DanRer7, [tetraodon] TetNig2, [fugu] Fr2, [stickleback] GasAcu1, [medaka] OryLat2, [lamprey] PerMar1, [lancelet] BraFlo1, [sea squirt] Ci2, [sea urchin] StrPur2, [D.simulans] DroSim1, [D.sechellia] DroSec1, [D.yakuba] DroYak2, [D.electa] DroEre1, [D.ananassae] DroAna2, [D.pseudoobscura] Dp3, [D.persimilis] DroPer1, [D. virilis] DroVir2, [D.mojavensis] DroMoj2, [D.grimshawi] DroGri1, [Anopheles mosquito] AnoGam1, [honey bee] ApiMel2, [C.brenneri] CaePb3, [C.briggsae] Cb3, [C.remanei] CaeRem3, [P.pacificus] PriPac1, [sea hare] AplCal1, [yeast] SacCer2
  • NEW (v0.2.1): Supporting Ruby 1.8.7 or later
  • NEW Adding to human Hg19 and Hg18, the following genome assemblies are supported: [mouse] Mm9, [fruitfly] Dm3, [C. elegans] Ce6, [genome assembly independent] Go, HgFixed, Proteome, UniProt, VisiGene
  • UPDATE (v0.2.0): Internal table class mapping algorithm are changed. Now table types are automatically detected and dynamically defined as classes. Previous versions used static class definition for all tables.
  • MODIFIED (v0.2.0): Bio::Ucsc::[Hg18|Hg19]::ReferenceSequence are removed. Use Bio::Ucsc::Reference instead. This class is more object-oriented.
  • MODIFIED (v0.1.0): The name of this library is now "Ruby UCSC API". The RubyGem name and the GitHub account and the library name are not changed.
  • MODIFIED (v0.1.0): Bio::Ucsc::[Hg18|Hg19]::Reference is replaced by Bio::Ucsc::[Hg18|Hg19]::ReferenceSequence.
  • UPDATE (v0.0.5): Almost all hg18 tables are supported.
  • UPDATE (v0.0.5): find_by_interval and find_all_by_interval class methods accept the "partial" option. Default is true. When "partial: false" is opted, return value will be only fully-included (non-partially-included) records.
  • UPDATE (v0.0.4): Almost all hg19 tables are supported. "filename" tables in ENCODE dataset are omitted. Each of them contains only single record of a path to the raw data file. Definitions of table relations are incomplete.
  • NEW (v0.0.3): Supporting locally-stored '2bit' files, which can be downloaded from the UCSC site, to retrieve referential sequence. Now supporting unknown "N" nucleotide blocks, however, "mask-blocks", which are shown in lower-case in UCSC's DNA function, are not supported yet.
  • MODIFIED (v0.0.3): For the "TABLE" class and the "column" column, <TABLE>.find_by_column retrieves a first record, and <TABLE>.find_all_by_column retrieves all the records as an Array.
  • NEW (v0.0.3-0.0.4): Supporting tables divided into each chromosome, such as "_RmsK" and "_gold". Actual names of them are like "chr1_Rmsk", "chr2_Rmsk"... They can be accessed without chromosome names; but with just like "Rmsk" and "Gold".