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'Data analysis/Variant database'에 해당되는 글 1건

  1. 2017.07.27 [dbsnp ] web mapping

[dbsnp ] web mapping

Data analysis/Variant database 2017. 7. 27. 14:54 
import sys
import urllib
import json
def readRSNumToJson(sRSNum):
    sURL = "http://grch37.rest.ensembl.org/variation/human/"+sRSNum+"?content-type=application/json"
    dRSNum = json.loads(urllib.urlopen(sURL).read().decode('utf-8'))
    return dRSNum
#end: def readRSNumToJson
if __name__ == "__main__":
	i = 0
	re = open('/Users/lsy/Desktop/neXtProt_rs_map.txt','a')
	f = open('/Users/lsy/Desktop/neXtProt_XML_MTsort_2.txt','r')
	for f_line in f.xreadlines():
		if i > 12871:
			f_sp = f_line.strip().split('\t')
			if f_sp[1].startswith('rs'):
				sRSNum = f_sp[1]
		    	dRSNum = readRSNumToJson(sRSNum)
		    	if len(dRSNum['mappings']) > 0:
		    		a = str(dRSNum['mappings'][0]['location'])
		    		b = str(dRSNum['mappings'][0]['allele_string'])
		    		re.write('\t'.join(f_sp + [a,b]) + '\n')
	    	print i
	    	i+= 1
	re.close()


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