counting number of SRA entries which came from same samples.

moshimokoukouyakyunojoshimanagergaNCBInoSRAwotsukattara.rb

# -*- coding: utf-8 -*-

require "open-uri"
require "json"
require "pp"

###
#  loading bullet
###

organism = "Homo+sapiens"
study_type = "Transcriptome+Analysis"

###
#   homuhomu
###

def countingSamples(namamono,sakusen) # betsuni method teigi suru hitsuyou nakatta kedo maa iiya mitame no mondai desyo konnnano

	mishima = "http://trace.ddbj.nig.ac.jp/DRASearch/"
	n = namamono.gsub("+","_")
	s = sakusen.gsub("+","_")
		
	# get full study list
	ground_floor = "#{mishima}query?organism=#{namamono}&study_type=#{sakusen}&show=100"
	deeper_underground = "#{mishima}query?organism=#{namamono}&study_type=#{sakusen}&show=100&page=2"
	list_study = URI("#{ground_floor}").read.scan(/href="(study¥?acc=.*)" target/).flatten
	list_study2 = URI("#{deeper_underground}").read.scan(/href="(study¥?acc=.*)" target/).flatten
	full_list = list_study.concat(list_study2)
	
	# save full sample list as json format file
	sample_id_full_list = full_list.map { |study_url|
		URI("#{mishima}#{study_url}").read.scan(/href="(sample¥?acc=.*)" target/)
	}.flatten
	open("./#{n}_#{s}_sample_id.json","w") { |f| f.puts JSON.dump(sample_id_full_list) }
	
	# make hash.. key: sample id, value: sample description
	srs_vs_desc = {}
	full_list.each { |study_url|
		srs_id = URI("#{mishima}#{study_url}").read.scan(/href="(sample¥?acc=.*)" target/).flatten
		
		srs_id.each { |sample_url|
			URI("#{mishima}#{sample_url}").read =‾ %r|Description</td><td>(.*)</td>|
			
			if $1 && !$1.empty?
				srs_vs_desc[sample_url] = $1
			else
				srs_vs_desc[sample_url] = "no description"
			end
		}
	}
	
	# save hash (but no need to save him)
	open("./#{n}_#{s}_srs_vs_desc.json","w") { |f| f.puts JSON.dump(srs_vs_desc) }
	
	# reverse hash.. key: sample description, value: sample id (array) 
	desc_vs_srs = {}
	srs_vs_desc.each_pair { |sample_url, desc|
		desc_vs_srs[desc] ||= []
		desc_vs_srs[desc].push(sample_url)
	}
	
	# count the number of sample ids which have same sample description
	desc_vs_numofsrs = {}
	desc_vs_srs.each_pair { |desc, sample_url|
		numofsrs = sample_url.length
		desc_vs_numofsrs[desc] = numofsrs
	}
	
	# sort hash by the number of sample ids
	sorted_list = desc_vs_numofsrs.to_a.sort { |a,b|
		(b[1] <=> a[1]) * 2 + (a[0] <=> b[0])
	}
	
	# fumu‾n
	return sorted_list

end

# kokode nanika tokubetsu na kotowo suru yotei datta to iu kotonisiteokou
pp countingSamples(organism,study_type)