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DAVID Web Service

2024-08-03 01:37:50   225人阅读

开始是打算用protein gi number，获得他们的go term。 本来想用uniprot来解决，不过想需要convert ID，这其中会导致有的ID对应不正常，一是缺失了；而是一对多，或者多对一。数据至少还要重新整理一次。

后来想到了david，先手动提交数据，而且要是多个物种的，他还不让整体分析，不能一次拿下所有结果，拿下后还需要重新解析一遍。发信问他们，他们也是自己先转ID再处理。

后来看到了david web service，用这个各异直接搞定，唯一的缺点是直接生成的结果变为文本保存后，不好解析。

于是用json重新保存一遍。

import syssys.path.append(‘../‘)import loggingimport traceback as tbimport suds.metrics as metricsfrom tests import *from suds import *from suds.client import Clientfrom datetime import datetimeerrors = 0setup_logging()logging.getLogger(‘suds.client‘).setLevel(logging.DEBUG)url = ‘http://david.abcc.ncifcrf.gov/webservice/services/DAVIDWebService?wsdl‘    print ‘url=%s‘ % url## create a service client using the wsdl.#client = Client(url)## print the service (introspection)#print client#authenticate user email print client.service.authenticate(‘XXX@XXX.XXX‘)#add a list #inputIds = ‘16077069,16077070,16077074,16077075,16077077,16077081,255767015,255767017,16077099,16077106,16077114,16077118,16077119,16077121‘inputIds = ‘16127995,16127996,16127997,16127998‘idType = ‘PROTEIN_GI_ACCESSION‘listName = ‘make_up‘listType = 0print client.service.addList(inputIds, idType, listName, listType)#print client.service.getDefaultCategoryNames()#getChartReportthd=0.1count = 2#print client.service.getChartReport(thd, count)#getTermClusterReportoverlap=3initialSeed = 3finalSeed = 3linkage = 0.5kappa = 20 #myresult = client.service.getTermClusterReport(overlap, initialSeed, finalSeed, linkage, kappa)mytable = client.service.getTableReport()#mylist = client.service.getListReport()with open(‘mytable.txt‘, ‘w‘) as f:    print >> f, mytablemylist1 = []for item in mytable:    tpdict = {}    tpdict[‘gi‘] = item[‘values‘][0][‘array‘][0]    tpdict[‘id‘] = item[‘geneObject‘][‘id‘]    tpdict[‘name‘] = item[‘name‘]    tplist = filter(lambda x: x[‘category‘].startswith(‘GOTERM‘), item[‘annotationRecords‘])    for i in tplist:        tpdict[i[‘category‘]] = i[‘terms‘]    mylist1.append(tpdict)f = open(‘test_json1.txt‘, ‘w‘)json.dump(mylist1, f, sort_keys = True, indent = 1)f.close()

 

DAVID Web Service


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