def testfasta_iter(self): fasta = open( self.seqfile ,'r' ) fasta_i = fasta_iter( fasta ) i= 0 for sequences in fasta_i: header, seq = sequences self.assertEqual( header , self.seqs[i][0] ) self.assertEqual( seq , self.seqs[i][1] ) i +=1 fasta.close()
def testrename_fasta(self): fasta_file = open( self.seqfile ,'r' ) renamed_fasta_name = os.path.join( TEST_DIR , 'fasta_renamed' ) renamed_fasta = open( renamed_fasta_name , 'w' ) mapping_file_name = os.path.join( TEST_DIR , 'mapping' ) mapping_file = open( mapping_file_name , 'w' ) rename_fasta(fasta_file , renamed_fasta , mapping_file ) fasta_file.close() renamed_fasta.close() mapping_file.close() old_fasta = open( self.seqfile ,'r' ) old_fasta_iter = fasta_iter( old_fasta ) new_fasta = open( renamed_fasta_name , 'r') new_fasta_iter = fasta_iter( new_fasta ) mapping_file = open( mapping_file_name , 'r') for l in mapping_file: old_header , old_seq = old_fasta_iter.next() new_header , new_seq = new_fasta_iter.next() new_map , old_map = l[:-1].split('\t') self.assertEqual( old_header , old_map ) self.assertEqual( new_header , new_map ) self.assertEqual( old_seq , new_seq )