bio-ucsc-api 0.0.1

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

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+# -*- coding: utf-8 -*-
+# = hg19/ccdsgene.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)
+#
+# = DESCRIPTION
+# From Structural Variants description page when clicking the "Describe 
+# table schema" in the table browser:
+#
+# = Table desfription in UCSC Table Browser
+# This track shows human genome high-confidence gene annotations from
+# the Consensus Coding Sequence (CCDS) project. This project is a
+# collaborative effort to identify a core set of human protein-coding
+# regions that are consistently annotated and of high quality. The
+# long-term goal is to support convergence towards a standard set of
+# gene annotations on the human genome.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class CcdsGene < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingCcdsBin
+        set_table_name 'ccdsGene'
+        set_primary_key nil
+      end # class CcdsGene
+    end # module Hg19
+  end # module Ucsc
+end # Bio

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

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+#
+# = hg19/cytoband.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 chromosome band track represents the approximate location of
+# bands seen on Giemsa-stained chromosomes. Chromosomes are displayed
+# in the browser with the short arm first. Cytologically identified
+# bands on the chromosome are numbered outward from the centromere on
+# the short (p) and long (q) arms. At low resolution, bands are
+# classified using the nomenclature [chromosome][arm][band], where
+# band is a single digit. Examples of bands on chromosome 3 include
+# 3p2, 3p1, cen, 3q1, and 3q2. At a finer resolution, some of the
+# bands are subdivided into sub-bands, adding a second digit to the
+# band number, e.g. 3p26. This resolution produces about 500 bands. A
+# final subdivision into a total of 862 sub-bands is made by adding a
+# period and another digit to the band, resulting in 3p26.3, 3p26.2,
+# etc.
+
+module Bio
+  module Ucsc
+    module Hg19
+      class CytoBand < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChrom
+        set_table_name 'cytoBand'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+#
+# = lib/ucsc/hg19/db_connection.rb - UCSC hg19 DB connection
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# Copyright::   Copyright (C) 2008
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'rubygems'
+require 'active_record'
+
+module Bio
+  module Ucsc
+
+    module Hg19
+      # = DESCRIPTION
+      # The Ucsc::Hg19::DBConnection is the actual connection established
+      # with the UCSC mysql server.
+
+      class DBConnection < ActiveRecord::Base
+        # = DESCRIPTION
+        # The Ucsc::Hg19::DBConnection#connect method makes the connection
+        # to the UCSC hg19 database.
+        #
+        # = USAGE
+        #  # Connect to the hg19
+        #  Ensembl::Core::DBConnection.connect
+        #
+        # ---
+        # *Arguments*: none
+        @@db_adapter  = 'mysql'
+        @@db_host     = 'genome-mysql.cse.ucsc.edu'
+        @@db_username = 'genome'
+        @@db_password = ''
+
+        cattr_accessor :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection(
+                               :adapter =>  @@db_adapter,
+                               :host =>     @@db_host,
+                               :database => 'hg19',
+                               :username => @@db_username,
+                               :password => @@db_password
+                               )
+        end
+      end
+    end # module Hg19
+    
+  end # module Ucsc
+end # module Bio

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

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+#
+# = hg19/dgv.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 displays copy number variants (CNVs),
+# insertions/deletions (InDels), inversions and inversion breakpoints
+# annotated by the Database of Genomic Variants (DGV), which contains
+# genomic variations observed in healthy individuals. DGV focuses on
+# structural variation, defined as genomic alterations that involve
+# segments of DNA that are larger than 1000 bp. Insertions/deletions
+# of 100 bp or larger are also included.
+#
+module Bio
+  module Ucsc
+    module Hg19
+      class Dgv < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'dgv'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+#
+# = hg19/ensgene.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
+# These gene predictions were generated by Ensembl.
+
+module Bio
+  module Ucsc
+    module Hg19
+      class EnsGene < DBConnection
+        extend  Bio::Ucsc::Hg19::QueryUsingTxBin
+        set_table_name 'ensGene'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+#
+# = hg19/gwascatalog.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 displays single nucleotide polymorphisms (SNPs)
+# identified by published Genome-Wide Association Studies (GWAS),
+# collected in the Catalog of Published Genome-Wide Association
+# Studies (www.genome.gov/gwastudies) at the National Human Genome
+# Research Institute (NHGRI). Some abbreviations are used above.
+# From http://www.genome.gov/gwastudies
+
+#
+module Bio
+  module Ucsc
+    module Hg19
+      class GwasCatalog < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'gwasCatalog'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapallelschimp.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.
+#
+# Ortho alleles for HapMap SNPs: Chimp
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapAllelesChimp < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+
+        set_table_name 'hapmapAllelesChimp'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapallelsmacaque.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.
+#
+# Ortho alleles for HapMap SNPs: Macaque
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapAllelesMacaque < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+
+        set_table_name 'hapmapAllelesMacaque'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpsasw.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.
+#
+# African Ancestry in SouthWestern United States (ASW)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsASW < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'hapmapSnpsASW'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpsceu.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.
+#
+# CEPH (Utah residents with ancestry from northern and western Europe) (CEU)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsCEU < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'hapmapSnpsCEU'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpschb.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.
+#
+# Han Chinese in Beijing, China (CHB)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsCHB < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'hapmapSnpsCHB'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpschd.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.
+#
+# Chinese Ancestry in Metropolitan Denver, CO, US (CHD)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsCHD < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'hapmapSnpsCHD'
+        set_primary_key nil
+      end
+    end
+  end
+end

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

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+# -*- coding: utf-8 -*-
+# = hg19/hapmapsnpsgih.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.
+#
+# Gujarati Indians in Houston, TX (GIH)
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class HapMapSnpsGIH < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'hapmapSnpsGIH'
+        set_primary_key nil
+      end
+    end
+  end
+end