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Versions: 10
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Contents
#
# The T25mersRepeats class is for the 25merRepeats table
#
module Bio
module Ucsc
module Ce6
class T25mersRepeats < DBConnection
self.table_name = "25mersRepeats"
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
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 = <<-SQL
chrom = :chrom
AND bin in (:bins)
AND ((chromStart BETWEEN :zstart AND :zend)
OR (chromEnd BETWEEN :zstart AND :zend)
OR (chromStart <= :zstart AND chromEnd >= :zend))
SQL
else
where = <<-SQL
chrom = :chrom
AND bin in (:bins)
AND ((chromStart BETWEEN :zstart AND :zend)
AND (chromEnd BETWEEN :zstart AND :zend))
SQL
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 # class
end # module Ce6
end # module Ucsc
end # module Bio
Version data entries
10 entries across 10 versions & 1 rubygems