def test_file_format_error(self): # given expected = FileFormatError file_path = 'wrongformat.txt' config_path = 'config.txt' # when rf = ReadFile() # then config = rf.get_config(config_path) self.assertRaises(expected, rf.seq_path, file_path, config)
def getCourseComment(self): courseCommentInfo = {} readFile = ReadFile() fileNamePaths = readFile.getFileName(self.fileDir) for fileNamePath in fileNamePaths: fileName = os.path.basename(fileNamePath).split(".")[0] comList = readFile.readFile(fileNamePath) courseCommentInfo.setdefault(fileName, comList) return courseCommentInfo
def test_too_long_sequence(self): # given expected = SequenceTooLongException file_path = 'longsequence.txt' config_path = 'config.txt' # when rf = ReadFile() config = rf.get_config(config_path) # then self.assertRaises(expected, rf.seq_path, file_path, config)
def test_read_sequence(self): # given config_path = 'config.txt' seq_path = 'a.txt' expected = 'GATTACA' # when rf = ReadFile() config = rf.get_config(config_path) seq = rf.seq_path(seq_path, config) # then self.assertEqual(seq, expected)
def getUserName(self): userInfo = {} filePath = "" readFile = ReadFile() nameList = readFile.readFile(filePath) db = DBconnect() dbc = db.dbConn() imageList = db.search(dbc) db.dbClose(dbc) for i in range(0, len(nameList)): userInfo.setdefault(nameList[0], imageList[0]) return userInfo
def test_read_config(self): # given config_path = 'config.txt' same = 5 diff = -5 gap_penalty = -2 max_seq_length = 100 max_number_path = 20 # when rf = ReadFile() config = rf.get_config(config_path) c = Config(same, diff, gap_penalty, max_seq_length, max_number_path) # then self.assertEqual(config.SAME, c.SAME) self.assertEqual(config.DIFF, c.DIFF) self.assertEqual(config.GAP_PENALTY, c.GAP_PENALTY) self.assertEqual(config.MAX_SEQ_LENGTH, c.MAX_SEQ_LENGTH) self.assertEqual(config.MAX_NUMBER_PATH, c.MAX_NUMBER_PATH)
def getCourseName(self): courseInfo = {} readFile = ReadFile() db = DBconnect() fileNamePaths = readFile.getFileName(self.fileDir) for fileNamePath in fileNamePaths: fileName = os.path.basename(fileNamePath).split(".")[0] sql = "select course_id from jh_course where title = '" + fileName + "'" dbc = db.dbConn() idList = db.search(dbc, sql) db.dbClose(dbc) courseInfo.setdefault(fileName, idList[0]) return courseInfo
def test_wrong_config_error(self): # given expected = WrongConfigInput file_path1 = 'wrongconfig1.txt' file_path2 = 'wrongconfig2.txt' file_path3 = 'wrongconfig3.txt' # when rf = ReadFile() # then self.assertRaises(expected, rf.get_config, file_path1) self.assertRaises(expected, rf.get_config, file_path2) self.assertRaises(expected, rf.get_config, file_path3)
def on_button_clicked(self): self.filename = InputLoadFile().filename self.data = ReadFile(self.filename).data # Second line : Text fields with X and Y hboxCoord = QHBoxLayout() label_min_x = QLabel("Min X : ") label_max_x = QLabel("Max X : ") self.textbox_min_x = QLineEdit() self.textbox_max_x = QLineEdit() hboxCoord.addWidget(label_min_x) hboxCoord.addWidget(self.textbox_min_x) hboxCoord.addWidget(label_max_x) hboxCoord.addWidget(self.textbox_max_x) hboxCoord.addStretch(1) # Forth line : Button Plot hbox_plot = QHBoxLayout() button_plot = QPushButton('Plot') button_plot.clicked.connect(self.launch_plot_window) hbox_plot.addStretch(1) hbox_plot.addWidget(button_plot) hbox_plot.addStretch(1) hbox_label_table = QHBoxLayout() label_table = QLabel("Values : ") hbox_label_table.addWidget(label_table) hbox_table = QHBoxLayout() tableWidget = QTableWidget() tableWidget.setRowCount(2) tableWidget.setColumnCount(len(self.data[0])) hbox_table.addWidget(tableWidget) for i in range(len(self.data[0])): tableWidget.setItem(0, i, QTableWidgetItem(str(self.data[0][i]))) tableWidget.setItem(1, i, QTableWidgetItem(str(self.data[1][i]))) self.vbox.addLayout(hboxCoord) self.vbox.addLayout(hbox_label_table) self.vbox.addLayout(hbox_table) self.vbox.addLayout(hbox_plot) self.textbox_min_x.setText(str(min(self.data[0]))) self.textbox_max_x.setText(str(max(self.data[0]))) self.label.setText(self.filename)
help='Path to the b sequence', required=True, dest='seq_b') parser.add_argument('-c', type=str, help='Path to the config file', required=True, dest='config_path') parser.add_argument('-o', type=str, help='Path to the output file', required=True, dest='output_path') args = parser.parse_args() rf = ReadFile() config = rf.get_config(args.config_path) nw = NeedlemanWunsh() mat, directmat = nw.calculate_matrix(rf.seq_path(args.seq_a, config), rf.seq_path(args.seq_b, config), config) score, alignments = nw.calculate_result(mat, directmat, rf.seq_path(args.seq_a, config), rf.seq_path(args.seq_b, config), config) # write results to file f = open(args.output_path, 'w') f.write('SCORE=' + str(score) + '\n') f.write('\n') for i in range(len(alignments)): f.write(alignments[i].res_a + '\n')