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')