bio-ucsc-api 0.3.1 → 0.4.0

data/lib/bio-ucsc/fr2/mrna.rb

@@ -12,25 +12,28 @@ module Bio
     module Fr2
 
       class Mrna
+        include DBConnector
+        DBConnection.database "fr2"
+
         KLASS = "Mrna"
         KLASS_S = "mrna"
 
         Bio::Ucsc::Fr2::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/fr2/rmsk.rb

@@ -13,21 +13,24 @@ module Bio
     module Fr2
 
       class Rmsk
+        include DBConnector
+        DBConnection.database "fr2"
+
         Bio::Ucsc::Fr2::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_Rmsk < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_rmsk"
-              set_primary_key nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_rmsk"
+              self.primary_key = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -60,13 +63,13 @@ AND  (genoEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_Rmsk")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_Rmsk")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/galgal3.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of the Chicken May 2006 (WUGSC 2.1/galGal3) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/galgal3/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -16,9 +16,12 @@ module Bio
 %w(chrM chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10
 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20
 chr21 chr22 chr23 chr24 chr25 chr26 chr27 chr28 chr32 chrW chrZ)
-      extend TableClassDetector
 
-      base = "#{File.dirname(__FILE__)}/galgal3"
+      extend TableClassDetector
+      include DBConnector
+      DBConnection.database "galGal3"
+ 
+      base = "#{::File.dirname(__FILE__)}/galgal3"
       autoload :ChainAnoCar1, "#{base}/chainanocar1"
       autoload :ChainAnoCar1Link, "#{base}/chainanocar1link"
       autoload :ChainBraFlo1, "#{base}/chainbraflo1"

data/lib/bio-ucsc/galgal3/chainanocar1.rb

@@ -12,25 +12,28 @@ module Bio
     module GalGal3
 
       class ChainAnoCar1
+        include DBConnector
+        DBConnection.database "galGal3"
+
         KLASS = "ChainAnoCar1"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::GalGal3::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/galgal3/chainanocar1link.rb

@@ -12,25 +12,28 @@ module Bio
     module GalGal3
 
       class ChainAnoCar1Link
+        include DBConnector
+        DBConnection.database "galGal3"
+
         KLASS = "ChainAnoCar1Link"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::GalGal3::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
 chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/galgal3/chainbraflo1.rb

@@ -12,25 +12,28 @@ module Bio
     module GalGal3
 
       class ChainBraFlo1
+        include DBConnector
+        DBConnection.database "galGal3"
+
         KLASS = "ChainBraFlo1"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::GalGal3::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/galgal3/chainbraflo1link.rb

@@ -12,25 +12,28 @@ module Bio
     module GalGal3
 
       class ChainBraFlo1Link
+        include DBConnector
+        DBConnection.database "galGal3"
+
         KLASS = "ChainBraFlo1Link"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::GalGal3::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
 chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/galgal3/chaincavpor3.rb

@@ -12,25 +12,28 @@ module Bio
     module GalGal3
 
       class ChainCavPor3
+        include DBConnector
+        DBConnection.database "galGal3"
+
         KLASS = "ChainCavPor3"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::GalGal3::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/galgal3/chaincavpor3link.rb

@@ -12,25 +12,28 @@ module Bio
     module GalGal3
 
       class ChainCavPor3Link
+        include DBConnector
+        DBConnection.database "galGal3"
+
         KLASS = "ChainCavPor3Link"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::GalGal3::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
 chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/galgal3/chaindanrer4.rb

@@ -12,25 +12,28 @@ module Bio
     module GalGal3
 
       class ChainDanRer4
+        include DBConnector
+        DBConnection.database "galGal3"
+
         KLASS = "ChainDanRer4"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::GalGal3::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)