def get_relatives(self, GeneID, alignmentType='both', blastThreshold=None, clustalwThreshold=None): self.c = db_conf.db_conf(username=self.username, password=self.password, server=self.server, db=self.database).get_cursor() self.db = pham.db(c=self.c) return phamerator_manage_db.get_relatives( self.c, GeneID, alignmentType=alignmentType, blastThreshold=blastThreshold, clustalwThreshold=clustalwThreshold)
def get_relatives(self, GeneID, alignmentType='both', blastThreshold=None, clustalwThreshold=None): self.c = db_conf.db_conf(username=self.username,password=self.password,server=self.server,db=self.database).get_cursor() self.db = pham.db(c = self.c) return phamerator_manage_db.get_relatives(self.c, GeneID, alignmentType=alignmentType, blastThreshold=blastThreshold, clustalwThreshold=clustalwThreshold)
#!/usr/bin/env python import db_conf import phamerator_manage_db import sys GeneID = sys.argv[1] c = db_conf.db_conf().get_cursor() relatives = phamerator_manage_db.get_relatives(c, GeneID, alignmentType='clustalw', clustalwThreshold=0.275) for r in relatives: print 'query:', r[0], 'subject:', r[1], 'score:', r[2]
#!/usr/bin/env python import db_conf import phamerator_manage_db import sys GeneID = sys.argv[1] c = db_conf.db_conf().get_cursor() relatives = phamerator_manage_db.get_relatives(c, GeneID, alignmentType="clustalw", clustalwThreshold=0.275) for r in relatives: print "query:", r[0], "subject:", r[1], "score:", r[2]