samples/hg19-sample.rb in bio-ucsc-api-0.2.1 vs samples/hg19-sample.rb in bio-ucsc-api-0.3.0

@@ -9,79 +9,63 @@
 #
 
 require File.dirname(__FILE__) + '/../lib/bio-ucsc'
 require 'nkf'
 
-include Bio::Ucsc
+include Bio
 
-Hg19::DBConnection.connect
+Ucsc::Hg19::DBConnection.connect
 
-itvs_a =
-  [Bio::GenomicInterval.parse("chr1:1-200,000"),
-   Bio::GenomicInterval.parse("chr2:1-200,000"),
-   Bio::GenomicInterval.parse("chr3:1-300,000"),
+gi_a =
+  [GenomicInterval.parse("chr1:1-200,000"),
+   GenomicInterval.parse("chr2:1-200,000"),
+   GenomicInterval.parse("chr3:1-300,000"),
   ]
 
 puts
 puts "Queries in Slice objects using 1-based [start,end] closed intervals"
 puts "Results in 0-based [start,end) half-open intervals"
 puts
 
-::puts "test 1 (hg19/RefGene) --- Bio::Ucsc::Hg19::RefGene.find_by_interval"
-results = itvs_a.map{|i|Hg19::RefGene.find_by_interval(i)}
+puts "test 1 (hg19/RefGene) --- Bio::Ucsc::Hg19::RefGene.with_interval"
+
+results = gi_a.map{|gi| Ucsc::Hg19::RefGene.with_interval(gi).find(:all)}
+
 puts "0-based interval\t1-based interval\tGene Symbol"
 results.flatten.each do |e|
   i = Bio::GenomicInterval.zero_based(e.chrom, e.txStart, e.txEnd)
   print "#{e.chrom}:#{e.txStart}-#{e.txEnd}\t"
   print "#{i.chrom}:#{i.chr_start}-#{i.chr_end}\t#{e.name2}\n"
 end
 
-#
-#
+#################################################################################
 
-itvs_b =
-  [Bio::GenomicInterval.parse("chr1:1-11,000"),
-   Bio::GenomicInterval.parse("chr2:1-11,000"),
-   Bio::GenomicInterval.parse("chr3:1-12,000"),
+gi_b =
+  [GenomicInterval.parse("chr1:1-11,000"),
+   GenomicInterval.parse("chr2:1-11,000"),
+   GenomicInterval.parse("chr3:1-12,000"),
   ]
 
 puts
-puts "test 2 (hg19/Snp131) --- Bio::Ucsc::Hg19::Snp131.find_by_interval" 
+puts "test 2 (hg19/Snp131) --- Bio::Ucsc::Hg19::Snp131.with_interval" 
 puts "0-based interval\t1-based interval\tdbSNP rs ID\tClass"
-results = itvs_b.map{|i|Hg19::Snp131.find_by_interval(i)}
+
+results = gi_b.map{|gi|Ucsc::Hg19::Snp131.with_interval(gi).find(:all)}
+
 results.flatten.each do |e|
   i = Bio::GenomicInterval.zero_based(e.chrom, e.chromStart, e.chromEnd)
   print "#{e.chrom}:#{e.chromStart}-#{e.chromEnd}\t"
   print "#{i.chrom}:#{i.chr_start}-#{i.chr_end}\t#{e.name}\t#{e[:class]}\n"
 end
 
+###############################################################################
 #
-#
 
 names = %w(rs56289060 rs62636508 rs28888107)
 
 puts
 puts "test 3 (hg19/Snp131) ---Bio::Ucsc::Hg19::Snp131.find_by_name"
 names.each do |n|
-  r =  Hg19::Snp131.find_by_name(n)
-  i = Bio::GenomicInterval.zero_based(r.chrom, r.chromStart, r.chromEnd)
+  r = Ucsc::Hg19::Snp131.find_by_name(n)
+  i = GenomicInterval.zero_based(r.chrom, r.chromStart, r.chromEnd)
   puts "Query: #{n}\t#{i.chrom}\t#{i.chr_start}\t#{i.chr_end}\t#{r[:class]}"
 end
-
-#
-#
-
-results = GbCdnaInfo.find([1,2,3,4,5], :include => :description)
-results.each{|e| puts "#{e.acc}\t#{e.description.name}"}
-
-p GbCdnaInfo.find_by_acc("AA411542",  :include => :description)
-
-results = KgXref.find_all_by_geneSymbol("TP53")
-results.each{|e| puts "#{e.mRNA}\t#{e.description}"}
-
-#
-#
-
-puts
-puts NKF.nkf("-wF72", RefSeqSummary.find_by_mrnaAcc("NM_000546").summary)
-puts
-puts NKF.nkf("-wF72", RefSeqSummary.find_by_mrnaAcc("NR_029476").summary)