bio-ucsc-api 0.0.3 → 0.0.4

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsmelanositesrep2.rb

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+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsmelanositesrep2.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsMelanoSitesRep2 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsMelanoSitesRep2'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsmelanositesrep3.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsmelanositesrep3.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsMelanoSitesRep3 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsMelanoSitesRep3'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnb4uwstamgrowprotsitesrep1.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnb4uwstamgrowprotsitesrep1.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNb4UwstamgrowprotSitesRep1 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNb4UwstamgrowprotSitesRep1'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnb4uwstamgrowprotsitesrep2.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnb4uwstamgrowprotsitesrep2.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNb4UwstamgrowprotSitesRep2 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNb4UwstamgrowprotSitesRep2'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnhauwstamgrowprotsitesrep1.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnhauwstamgrowprotsitesrep1.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNhaUwstamgrowprotSitesRep1 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNhaUwstamgrowprotSitesRep1'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnhauwstamgrowprotsitesrep2.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnhauwstamgrowprotsitesrep2.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNhaUwstamgrowprotSitesRep2 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNhaUwstamgrowprotSitesRep2'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnhbeuwstamgrowprotsitesrep1.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnhbeuwstamgrowprotsitesrep1.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNhbeUwstamgrowprotSitesRep1 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNhbeUwstamgrowprotSitesRep1'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnhbeuwstamgrowprotsitesrep2.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnhbeuwstamgrowprotsitesrep2.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNhbeUwstamgrowprotSitesRep2 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNhbeUwstamgrowprotSitesRep2'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnhdfneouwstamgrowprotsitesrep1.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnhdfneouwstamgrowprotsitesrep1.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNhdfneoUwstamgrowprotSitesRep1 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNhdfneoUwstamgrowprotSitesRep1'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnhdfneouwstamgrowprotsitesrep2.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnhdfneouwstamgrowprotsitesrep2.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNhdfneoUwstamgrowprotSitesRep2 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNhdfneoUwstamgrowprotSitesRep2'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio

data/lib/bio-ucsc/hg19/wgencodehaibmethylrrbsnt2d1yalegrowprotsitesrep1.rb

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# = hg19/wgencodehaibmethylrrbsnt2d1yalegrowprotsitesrep1.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 reports the percentage of DNA molecules that exhibit
+# cytosine methylation at specific CpG dinucleotides. In general, DNA
+# methylation within a gene's promoter is associated with gene
+# silencing, and DNA methylation within the exons and introns of a
+# gene is associated with gene expression. Proper regulation of DNA
+# methylation is essential during development and aberrant DNA
+# methylation is a hallmark of cancer. DNA methylation status is
+# assayed at more than 500,000 CpG dinucleotides in the genome using
+# Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is
+# digested with the methyl-insensitive restriction enzyme MspI, small
+# genomic DNA fragments are purified by gel electrophoresis, and then
+# used to construct an Illumina sequencing library. The library
+# fragments are treated with sodium bisulfite and amplified by PCR to
+# convert every unmethylated cytosine to a thymidine while leaving
+# methylated cytosines intact. The sequenced fragments are aligned to
+# a customized reference genome sequence and for each assayed CpG we
+# report the number of sequencing reads covering that CpG and the
+# percentage of those reads that are methylated.
+#
+# = ommitted dynamic method(s) due to the method name collision
+#  none
+
+module Bio
+  module Ucsc
+    module Hg19
+      class WgEncodeHaibMethylRrbsNt2d1YalegrowprotSitesRep1 < DBConnection
+        extend Bio::Ucsc::Hg19::QueryUsingChromBin
+        set_table_name 'wgEncodeHaibMethylRrbsNt2d1YalegrowprotSitesRep1'
+        set_primary_key nil
+      end 
+    end # module Hg19
+  end # module Ucsc
+end # Bio