Module: Bio::Ucsc::TableClassDetector
- Included in:
- AilMel1, AnoCar2, AnoGam1, ApiMel2, AplCal1, BosTau4, BraFlo1, CaeJap1, CaePb2, CaeRem3, CalJac3, CanFam2, CavPor3, Cb3, Ce6, Ci2, DanRer7, Dm3, Dp3, DroAna2, DroEre1, DroGri1, DroMoj2, DroPer1, DroSec1, DroSim1, DroVir2, DroYak2, EquCab2, FelCat4, Fr2, GalGal4, GasAcu1, Go, Hg18, Hg19, Hg38, HgFixed, LoxAfr3, Mm10, Mm9, MonDom5, OrnAna1, OryCun2, OryLat2, OviAri1, PanTro3, PetMar1, PonAbe2, PriPac1, Proteome, RheMac2, Rn4, Rn5, SacCer2, StrPur2, SusScr2, TaeGut1, TetNig2, UniProt, VisiGene, XenTro2
- Defined in:
- lib/bio-ucsc/table_class_detector.rb
Constant Summary collapse
- RESERVED_METHODS =
['func', 'attribute', 'valid', 'validate', 'class', 'method', 'methods', 'type']
- UPPERCASED_TABLE_PREFIX =
['HInv', 'NIAGene']
- COMMON_CLASS_METHODS =
%! def self.find_by_interval(interval, opt = {:partial => true}) interval = Bio::Ucsc::Gi.wrap(interval) find_first_or_all_by_interval(interval, :first, opt) end def self.find_all_by_interval(interval, opt = {:partial => true}) interval = Bio::Ucsc::Gi.wrap(interval) find_first_or_all_by_interval(interval, :all, opt) end !
- PARAMETERS =
%! { :chrom => interval.chrom, :bins => interval.bin_all, :zstart => interval.zero_start, :zend => interval.zero_end, } !
Instance Method Summary collapse
-
#bed(sym, opts = {:bin => true}) ⇒ Object
BED: Browser Extensible Description format interval search using chrom/chromStart/chromEnd.
- #const_missing(sym) ⇒ Object
-
#genepred(sym, opts = {:bin => true}) ⇒ Object
genePred: Gene and gene-prediction features interval search using chrom/txStart/txEnd.
-
#generic(sym) ⇒ Object
generic: tables without interval serarch supported also used to prefetch table column names.
-
#psl(sym, opts = {:bin => true}) ⇒ Object
PSL: Pattern Space Layout interval search using tName/tStart/tEnd.
-
#rmsk(sym, opts = {:bin => true}) ⇒ Object
rmsk: Repeatmasker .out file interval search using genoName/genoStart/genoEnd.
Instance Method Details
#bed(sym, opts = {:bin => true}) ⇒ Object
BED: Browser Extensible Description format interval search using chrom/chromStart/chromEnd
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# File 'lib/bio-ucsc/table_class_detector.rb', line 153 def bed(sym, opts={:bin => true}) if opts[:bin] chrom_bin = "chrom = :chrom AND bin in (:bins) " else chrom_bin = "chrom = :chrom " end %! class #{uphead(sym)} < DBConnection self.table_name = "#{downhead(sym)}" #{delete_reserved_methods} #{COMMON_CLASS_METHODS} def self.with_interval(interval) interval = Bio::Ucsc::Gi.wrap(interval) where( "#{chrom_bin}" + "AND ( " + "(chromStart BETWEEN :zstart AND :zend)" + "OR (chromEnd BETWEEN :zstart AND :zend)" + "OR (chromStart <= :zstart AND chromEnd >= :zend) )", #{PARAMETERS}) end def self.with_interval_excl(interval) interval = Bio::Ucsc::Gi.wrap(interval) where( "#{chrom_bin}" + "AND ( " + "(chromStart BETWEEN :zstart AND :zend) " + "AND (chromEnd BETWEEN :zstart AND :zend) )", #{PARAMETERS}) end def self.find_first_or_all_by_interval(interval, first_all, opt) interval = Bio::Ucsc::Gi.wrap(interval) zstart = interval.zero_start zend = interval.zero_end if opt[:partial] == true where = "#{chrom_bin}" + "AND ( " + "(chromStart BETWEEN :zstart AND :zend) " + "OR (chromEnd BETWEEN :zstart AND :zend) " + "OR (chromStart <= :zstart AND chromEnd >= :zend) )" else where = "#{chrom_bin}" + "AND ( " + "(chromStart BETWEEN :zstart AND :zend)" + "AND (chromEnd BETWEEN :zstart AND :zend))" end cond = { :chrom => interval.chrom, :bins => Ucsc::UcscBin.bin_all(zstart, zend), :zstart => zstart, :zend => zend, } self.find(first_all, { :select => "*", :conditions => [where, cond], }) end end ! end |
#const_missing(sym) ⇒ Object
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# File 'lib/bio-ucsc/table_class_detector.rb', line 43 def const_missing(sym) module_eval generic(sym) col_names = const_get(sym).columns.map{|x|x.name} case when (["bin", "tName", "tStart", "tEnd"] - col_names).empty? module_eval psl(sym, :bin => true) when (["bin", "tName", "tStart", "tEnd"] - col_names) == ["bin"] module_eval psl(sym, :bin => false) when (["bin", "chrom", "chromStart", "chromEnd"] - col_names).empty? module_eval bed(sym, :bin => true) when (["bin", "chrom", "chromStart", "chromEnd"] - col_names) == ["bin"] module_eval bed(sym, :bin => false) when (["bin", "chrom", "txStart", "txEnd"] - col_names).empty? module_eval genepred(sym, :bin => true) when (["bin", "chrom", "txStart", "txEnd"] - col_names) == ["bin"] module_eval genepred(sym, :bin => false) when (["bin", "genoName", "genoStart", "genoEnd"] - col_names).empty? module_eval rmsk(sym, :bin => true) when (["bin", "genoName", "genoStart", "genoEnd"] - col_names) == ["bin"] module_eval rmsk(sym, :bin => false) end const_get(sym) end |
#genepred(sym, opts = {:bin => true}) ⇒ Object
genePred: Gene and gene-prediction features interval search using chrom/txStart/txEnd
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# File 'lib/bio-ucsc/table_class_detector.rb', line 221 def genepred(sym, opts={:bin => true}) if opts[:bin] chrom_bin = "chrom = :chrom AND bin in (:bins) " else chrom_bin = "chrom = :chrom " end %! class #{uphead(sym)} < DBConnection self.table_name = "#{downhead(sym)}" #{delete_reserved_methods} #{COMMON_CLASS_METHODS} def self.with_interval(interval) interval = Bio::Ucsc::Gi.wrap(interval) where( "#{chrom_bin}" + "AND ( " + "(txStart BETWEEN :zstart AND :zend) " + "OR (txEnd BETWEEN :zstart AND :zend) " + "OR (txStart <= :zstart AND txEnd >= :zend) )", #{PARAMETERS}) end def self.with_interval_excl(interval) interval = Bio::Ucsc::Gi.wrap(interval) where( "#{chrom_bin}" + "AND ( " + "(txStart BETWEEN :zstart AND :zend) " + "AND (txEnd BETWEEN :zstart AND :zend) )", #{PARAMETERS}) end def self.find_first_or_all_by_interval(interval, first_all, opt) interval = Bio::Ucsc::Gi.wrap(interval) zstart = interval.zero_start zend = interval.zero_end if opt[:partial] == true where = "#{chrom_bin}" + "AND ( " + "(txStart BETWEEN :zstart AND :zend)" + "OR (txEnd BETWEEN :zstart AND :zend)" + "OR (txStart <= :zstart AND txEnd >= :zend))" else where = "#{chrom_bin}" + "AND ( " + "(txStart BETWEEN :zstart AND :zend)" + "AND (txEnd BETWEEN :zstart AND :zend) )" end cond = { :chrom => interval.chrom, :bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend), :zstart => zstart, :zend => zend, } self.find(first_all, { :select => "*", :conditions => [where, cond], }) end def exons_raw starts = exonStarts.split(",").map{|x|Integer(x)} ends = exonEnds.split(",").map{|x|Integer(x)} starts.zip(ends).map do |x| Bio::GenomicInterval.zero_based(chrom, x[0], x[1]) end end def exons return @exons if @exons if strand == "+" @exons = exons_raw else @exons = exons_raw.reverse end @exons end def introns return @introns if @introns if exonCount == 1 @introns = [] return @introns end @introns = Array.new exons_raw.each_cons(2) do |ex1, ex2| @introns << Bio::GenomicInterval.zero_based(chrom, ex1.zero_end, ex2.zero_start) end @introns = @introns.reverse if strand == "-" @introns end def cdses return @cdses if @cdses if cdsStart == cdsEnd # gene without CDSes @cdses = [] return @cdses end cdses_exons_plus = exons_raw.reject do |x| x.zero_end < cdsStart || cdsEnd < x.zero_start end cdses_plus = cdses_exons_plus.map do |x| zstart = x.zero_start zstart = cdsStart if x.zero_start < cdsStart zend = x.zero_end zend = cdsEnd if cdsEnd < x.zero_end Bio::GenomicInterval.zero_based(chrom, zstart, zend) end if strand == "+" @cdses = cdses_plus else @cdses = cdses_plus.reverse end @cdses end # def cdses alias :cdss :cdses end # class ! end |
#generic(sym) ⇒ Object
generic: tables without interval serarch supported also used to prefetch table column names
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# File 'lib/bio-ucsc/table_class_detector.rb', line 74 def generic(sym) %! class #{uphead(sym)} < DBConnection self.table_name = "#{downhead(sym)}" #{delete_reserved_methods} end ! end |
#psl(sym, opts = {:bin => true}) ⇒ Object
PSL: Pattern Space Layout interval search using tName/tStart/tEnd
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# File 'lib/bio-ucsc/table_class_detector.rb', line 85 def psl(sym, opts={:bin => true}) if opts[:bin] chrom_bin = "tName = :chrom AND bin in (:bins) " else chrom_bin = "tName = :chrom " end %! class #{uphead(sym)} < DBConnection self.table_name = "#{downhead(sym)}" #{delete_reserved_methods} #{COMMON_CLASS_METHODS} def self.with_interval(interval) interval = Bio::Ucsc::Gi.wrap(interval) where( "#{chrom_bin}" + "AND ( " + "(tStart BETWEEN :zstart AND :zend) " + "OR (tEnd BETWEEN :zstart AND :zend) " + "OR (tStart <= :zstart AND tEnd >= :zend) )", #{PARAMETERS}) end def self.with_interval_excl(interval) interval = Bio::Ucsc::Gi.wrap(interval) where( "#{chrom_bin}" + "AND ( " + "(tStart BETWEEN :zstart AND :zend)" + "AND (tEnd BETWEEN :zstart AND :zend) )", #{PARAMETERS}) end def self.find_first_or_all_by_interval(interval, first_all, opt) interval = Bio::Ucsc::Gi.wrap(interval) zstart = interval.zero_start zend = interval.zero_end if opt[:partial] == true where = "#{chrom_bin}" + "AND ( " + "(tStart BETWEEN :zstart AND :zend) " + "OR (tEnd BETWEEN :zstart AND :zend) " + "OR (tStart <= :zstart AND tEnd >= :zend) )" else where = "#{chrom_bin}" + "AND ( " + "(tStart BETWEEN :zstart AND :zend) " + "AND (tEnd BETWEEN :zstart AND :zend) )" end cond = { :chrom => interval.chrom, :bins => Ucsc::UcscBin.bin_all(zstart, zend), :zstart => zstart, :zend => zend,} self.find(first_all, { :select => "*", :conditions => [where, cond], }) end end ! end |
#rmsk(sym, opts = {:bin => true}) ⇒ Object
rmsk: Repeatmasker .out file interval search using genoName/genoStart/genoEnd
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# File 'lib/bio-ucsc/table_class_detector.rb', line 350 def rmsk(sym, opts={:bin => true}) if opts[:bin] chrom_bin = "genoName = :chrom AND bin in (:bins) " else chrom_bin = "genoName = :chrom " end %! class #{uphead(sym)} < DBConnection self.table_name = "#{downhead(sym)}" #{delete_reserved_methods} #{COMMON_CLASS_METHODS} def self.with_interval(interval) interval = Bio::Ucsc::Gi.wrap(interval) where( "#{chrom_bin}" + "AND ( " + "(genoStart BETWEEN :zstart AND :zend)" + "OR (genoEnd BETWEEN :zstart AND :zend)" + "OR (genoStart <= :zstart AND genoEnd >= :zend) )", #{PARAMETERS}) end def self.with_interval_excl(interval) interval = Bio::Ucsc::Gi.wrap(interval) where( "#{chrom_bin}" + "AND ( " + "(genoStart BETWEEN :zstart AND :zend)" + "AND (genoEnd BETWEEN :zstart AND :zend) )", #{PARAMETERS}) end def self.find_first_or_all_by_interval(interval, first_all, opt) interval = Bio::Ucsc::Gi.wrap(interval) zstart = interval.zero_start zend = interval.zero_end if opt[:partial] == true where = "#{chrom_bin}" + "AND ( " + "(genoStart BETWEEN :zstart AND :zend) " + "OR (genoEnd BETWEEN :zstart AND :zend) " + "OR (genoStart <= :zstart AND genoEnd >= :zend) )" else where = "#{chrom_bin}" + "AND ( " + "(genoStart BETWEEN :zstart AND :zend) " + "AND (genoEnd BETWEEN :zstart AND :zend) )" end cond = { :chrom => interval.chrom, :bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend), :zstart => zstart, :zend => zend, } self.find(first_all, { :select => "*", :conditions => [where, cond], }) end end ! end |