testAnnotator.py 文件源码

def batchTestHelper(self, modFile, pool, refLens):                
        tmpName = tempfile.mkstemp('.tsv')[1]
        tmpfp = open(tmpName, 'wb')
        for line in modFile:
            tmpfp.write(line)
        tmpfp.close()
        pysam.tabix_index(tmpName, force=True, seq_col=1, start_col=2, end_col=2, 
                      meta_char='#', zerobased=True)
        tmpName += '.gz'
        modFile.close()

        self.chromoID = '1'
        self.modobj = mod.Mod(tmpName)
        self.modobj.load(self.chromoID)

        for tup in pool:       
            bamIter=[Read(tup[0], tup[1]+1, tup[2]) for tup in pool]        

        a = annot.Annotator(self.chromoID, refLens[self.chromoID],
                                self.modobj, bamIter)
        results = a.execute()

        for i,res in enumerate(results):            
            self.assertEqual(polish(res[0]),pool[i][3])
            self.assertEqual(res[1], pool[i][4])
            self.assertEqual(res[2], pool[i][5])
            self.assertEqual(res[3], pool[i][6])
            self.assertEqual(res[4], pool[i][7])

        os.remove(tmpName)
        os.remove(tmpName+'.tbi')