bio-ucsc-api 0.0.1

data/lib/bio-ucsc/hg19/hapmapsnpsjpt.rb

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpsjpt.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki
+#                <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# The HapMap Project identified a set of approximately four million
+# common SNPs, and genotyped these SNPs in four populations in Phase
+# II of the project. In Phase III, it genotyped approximately 1.4 to
+# 1.5 million SNPs in eleven populations. This track shows the
+# combined data from Phases II and III. The intent is that this data
+# can be used as a reference for future studies of human disease. This
+# track displays the genotype counts and allele frequencies of those
+# SNPs, and (when available) shows orthologous alleles from the chimp
+# and macaque reference genome assemblies.
+#
+# Japanese in Tokyo, Japan (JPT)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsJPT < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'hapmapSnpsJPT'
+        set_primary_key nil
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/hapmapsnpslwk.rb

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpslwk.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki
+#                <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# The HapMap Project identified a set of approximately four million
+# common SNPs, and genotyped these SNPs in four populations in Phase
+# II of the project. In Phase III, it genotyped approximately 1.4 to
+# 1.5 million SNPs in eleven populations. This track shows the
+# combined data from Phases II and III. The intent is that this data
+# can be used as a reference for future studies of human disease. This
+# track displays the genotype counts and allele frequencies of those
+# SNPs, and (when available) shows orthologous alleles from the chimp
+# and macaque reference genome assemblies.
+#
+# Luhya in Webuye, Kenya (LWK)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsLWK < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+
+        set_table_name 'hapmapSnpsLWK'
+        set_primary_key nil
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/hapmapsnpsmex.rb

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpsmex.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki
+#                <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# The HapMap Project identified a set of approximately four million
+# common SNPs, and genotyped these SNPs in four populations in Phase
+# II of the project. In Phase III, it genotyped approximately 1.4 to
+# 1.5 million SNPs in eleven populations. This track shows the
+# combined data from Phases II and III. The intent is that this data
+# can be used as a reference for future studies of human disease. This
+# track displays the genotype counts and allele frequencies of those
+# SNPs, and (when available) shows orthologous alleles from the chimp
+# and macaque reference genome assemblies.
+#
+# Mexican Ancestery in Los Angeles, CA, US (MEX)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsMEX < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+
+        set_table_name 'hapmapSnpsMEX'
+        set_primary_key nil
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/hapmapsnpsmkk.rb

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpsmkk.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki
+#                <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# The HapMap Project identified a set of approximately four million
+# common SNPs, and genotyped these SNPs in four populations in Phase
+# II of the project. In Phase III, it genotyped approximately 1.4 to
+# 1.5 million SNPs in eleven populations. This track shows the
+# combined data from Phases II and III. The intent is that this data
+# can be used as a reference for future studies of human disease. This
+# track displays the genotype counts and allele frequencies of those
+# SNPs, and (when available) shows orthologous alleles from the chimp
+# and macaque reference genome assemblies.
+#
+# Masai in Kinyawa, Kenya (MKK)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsMKK < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+
+        set_table_name 'hapmapSnpsMKK'
+        set_primary_key nil
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/hapmapsnpstsi.rb

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpstsi.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki
+#                <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# The HapMap Project identified a set of approximately four million
+# common SNPs, and genotyped these SNPs in four populations in Phase
+# II of the project. In Phase III, it genotyped approximately 1.4 to
+# 1.5 million SNPs in eleven populations. This track shows the
+# combined data from Phases II and III. The intent is that this data
+# can be used as a reference for future studies of human disease. This
+# track displays the genotype counts and allele frequencies of those
+# SNPs, and (when available) shows orthologous alleles from the chimp
+# and macaque reference genome assemblies.
+#
+# Toscani in Italia (TSI)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsTSI < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+
+        set_table_name 'hapmapSnpsTSI'
+        set_primary_key nil
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/hapmapsnpsyri.rb

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpsyari.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki
+#                <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# The HapMap Project identified a set of approximately four million
+# common SNPs, and genotyped these SNPs in four populations in Phase
+# II of the project. In Phase III, it genotyped approximately 1.4 to
+# 1.5 million SNPs in eleven populations. This track shows the
+# combined data from Phases II and III. The intent is that this data
+# can be used as a reference for future studies of human disease. This
+# track displays the genotype counts and allele frequencies of those
+# SNPs, and (when available) shows orthologous alleles from the chimp
+# and macaque reference genome assemblies.
+#
+# Yoruba in Ibadan, Nigeria (YRI)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsYRI < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+
+        set_table_name 'hapmapSnpsYRI'
+        set_primary_key nil
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/knowngene.rb

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+# -*- coding: utf-8 -*-
+# = hg19/knowngene.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# The UCSC Genes track shows gene predictions based on data from
+# RefSeq, Genbank, CCDS and UniProt. This is a moderately
+# conservative set of predictions, requiring the support of one
+# GenBank RNA sequence plus at least one additional line of
+# evidence. The RefSeq RNAs are an exception to this, requiring no
+# additional evidence. The track includes both protein-coding and
+# putative non-coding transcripts. Some of these non-coding
+# transcripts may actually code for protein, but the evidence for the
+# associated protein is weak at best. Compared to RefSeq, this gene
+# set has generally about 10% more protein-coding genes,
+# approximately five times as many putative non-coding genes, and
+# about twice as many splice variants.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class KnownGene < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingTx
+        set_table_name 'knownGene'
+        set_primary_key nil
+      end # class KnownGene
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/omimgene.rb

@@ -0,0 +1,25 @@
+#
+# = hg19/omimgene.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# This track shows the positions of canonical UCSC genes that have
+# been associated with identifiers in the Online Mendelian Inheritance
+# in Man (OMIM) database. The associations were obtained from RefSeq
+# and UniProt annotations. To simplify the track, annotations on
+# splice variants have been collapsed so that only canonical UCSC
+# splice variants are displayed.
+
+module Bio
+  module Ucsc
+    module Hg19
+      class OmimGene < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'omimGene'
+        set_primary_key nil
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/phastconselements46wayprimates.rb

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+#
+# = hg19/phastconelements46wayprimates.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table description in UCSC Table Browser This track shows multiple
+# alignments of 46 vertebrate species and measurements of evolutionary
+# conservation using two methods (phastCons and phyloP) from the PHAST
+# package, for all species (vertebrate) and two subsets (primate and
+# placental mammal). The multiple alignments were generated using
+# multiz and other tools in the UCSC/Penn State Bioinformatics
+# comparative genomics alignment pipeline. Conserved elements
+# identified by phastCons are also displayed in this track.
+#
+
+module Bio
+  module Ucsc
+    module Hg19
+      class PhastConsElements46wayPrimates < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'phastConsElements46wayPrimates'
+        set_primary_key nil
+       end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/phylop46wayprimates.rb

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+#
+# = hg19/phylop46wayprimate.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table description in UCSC Table Browser This track shows multiple
+# alignments of 46 vertebrate species and measurements of evolutionary
+# conservation using two methods (phastCons and phyloP) from the PHAST
+# package, for all species (vertebrate) and two subsets (primate and
+# placental mammal). The multiple alignments were generated using
+# multiz and other tools in the UCSC/Penn State Bioinformatics
+# comparative genomics alignment pipeline. Conserved elements
+# identified by phastCons are also displayed in this track.
+#
+
+module Bio
+  module Ucsc
+    module Hg19
+      class PhyloP46wayPrimates < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'phyloP46wayPrimates'
+        set_primary_key nil
+       end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/refgene.rb

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+# = hg19/refgene.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+#  Copyright (C) 2008 Jan Aerts <jan.aerts@gmail.com>
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# The RefSeq Genes track shows known human protein-coding and
+# non-protein-coding genes taken from the NCBI RNA reference sequences
+# collection (RefSeq). The data underlying this track are updated
+# daily.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class RefGene < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingTxBin
+        set_table_name 'refGene'
+        set_primary_key nil
+      end # class RefGene
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/rmsk.rb

@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+# = hg19/rmsk.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# This track was created by using Arian Smit's RepeatMasker program,
+# which screens DNA sequences for interspersed repeats and low
+# complexity DNA sequences. The program outputs a detailed annotation
+# of the repeats that are present in the query sequence (represented
+# by this track), as well as a modified version of the query sequence
+# in which all the annotated repeats have been masked (generally
+# available on the Downloads page). RepeatMasker uses the RepBase
+# library of repeats from the Genetic Information Research Institute
+# (GIRI). RepBase is described in Jurka, J. (2000) in the References
+# section below.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class Rmsk < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingGenoBin
+        set_table_name 'rmsk'
+        set_primary_key nil
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/snp131.rb

@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+# = hg19/snp131.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+#  Copyright (C) 2008 Jan Aerts <jan.aerts@gmail.com>
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table desfription in UCSC Table Browser
+# This track contains information about single nucleotide
+# polymorphisms and small insertions and deletions (indels) —
+# collectively Simple Nucleotide Polymorphisms — from dbSNP build
+# 131, available from ftp.ncbi.nih.gov/snp.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  use results[:valid] instead of results.valid
+#  use results[:class] instead of results.class
+
+module Bio
+  module Ucsc
+    module Hg19
+      class Snp131 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'snp131'
+        set_primary_key nil
+        columns_hash.delete("valid")
+        columns_hash.delete("class")
+      end
+    end
+  end
+end

data/lib/bio-ucsc/hg19/snp132.rb

@@ -0,0 +1,31 @@
+#
+# = hg19/snp132.rb
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# = Table description in UCSC Table Browser
+# This track contains information about a subset of the single
+# nucleotide polymorphisms and small insertions and deletions (indels)
+# -- collectively Simple Nucleotide Polymorphisms -- from dbSNP
+# build 132, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a
+# minor allele frequency of at least 1% and are mapped to a single
+# location in the reference genome assembly are included in this
+# subset. Frequency data are not available for all SNPs, so this subset
+# is incomplete.
+# 
+# SNPs(132): all dbSNP build 132
+
+module Bio
+  module Ucsc
+    module Hg19
+      class Snp132 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'snp132'
+        set_primary_key nil
+        columns_hash.delete("valid")
+        columns_hash.delete("class")
+      end
+    end
+  end
+end