Change Log¶ ↑
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UPDATE (v.0.6.5) Support Zebrafish DanRer10 and DanRer11 references.
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UPDATE (v.0.6.4) Support Ruby 2.4 by using Rails 4.2 and the MySql2 gem v0.4 at BioHackathon2017 20
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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”.
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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.
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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.
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BUG-FIX (v 0.5.3): Support ActiveRecord/ActiveSupport version 3 only.
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UPDATE (v 0.5.3): The Rat Rn5 database is supported.
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UPDATE (v 0.5.3): Bug-fix and update to pass all specs on Ruby 2.0.0-p0.
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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.
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BUG-FIX (v.0.5.0): Connecting multiple databeses simultaneously now works well.
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NEW (v0.5.0): Support automatic definitions of table association using the “all.joiner” schema file.
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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 ofBio::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” andBio::GenomicInterval
objects -
BUG-FIX (v0.4.0): By using the safe_attribute gem, newest version of ActiveRecord is supported.
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UPDATE (v0.4.0):
Bio::Ucsc::Reference
is moved toBio::Ucsc::File::Twobit
(backward compatibility is kept).Bio::Ucsc::File::Twobit.open
andBio::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.
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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.
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BUG-FIX (v0.3.1): “func” fields in tables did not work. The bug was fixed.
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BUG-FIX (v0.3.1): PredGene-type tables without the bin index did not work. The bug was fixed.
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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.
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NEW (v0.3.0):
Bio::GenomicInterval#bin_all
andBio::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
. Tryjruby -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
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NEW (v0.2.1): Supporting Ruby 1.8.7 or later
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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
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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.
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MODIFIED (v0.2.0): Bio::Ucsc::::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.
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MODIFIED (v0.1.0):
Bio::Ucsc::[Hg18|Hg19]::Reference
is replaced byBio::Ucsc::[Hg18|Hg19]::ReferenceSequence
. -
UPDATE (v0.0.5): Almost all hg18 tables are supported.
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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.
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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.
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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.
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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”.