def search_organism(organism):
k = KEGG()
return k.lookfor_organism(organism)
class NewGenome(QtWidgets.QMainWindow):
def __init__(self, info_path):
super(NewGenome, self).__init__()
uic.loadUi('NewGenome.ui', self)
self.setWindowTitle('New Genome')
self.k = KEGG()
self.info_path = info_path
#---Button Modifications---#
self.setWindowIcon(Qt.QIcon("cas9image.png"))
self.whatsthisButton.clicked.connect(self.whatsthisclicked)
self.KeggSearchButton.clicked.connect(self.updatekegglist)
self.resetButton.clicked.connect(self.reset)
self.submitButton.clicked.connect(self.submit)
self.browseForFile.clicked.connect(self.selectFasta)
self.NCBI_File_Search.clicked.connect(self.prep_ncbi_search)
self.JobsQueueBox.setReadOnly(True)
self.output_browser.setText("Waiting for program initiation...")
self.CompletedJobs.setText(" ")
self.contButton.clicked.connect(self.continue_to_main)
self.comboBoxEndo.currentIndexChanged.connect(self.endo_settings)
self.runButton.clicked.connect(self.run_jobs)
self.clearButton.clicked.connect(self.clear_job_queue)
self.viewStatButton.setEnabled(False)
self.JobsQueue = [] # holds Job classes.
self.Endos = dict()
self.file = ""
self.process = QtCore.QProcess()
self.process.setProcessChannelMode(QtCore.QProcess.MergedChannels)
self.process.finished.connect(self.upon_process_finishing)
self.seqTrans = SeqTranslate()
self.first = False
#show functionalities on window
self.fillEndo()
#self.show()
self.num_chromo_next = False
####---FUNCTIONS TO RUN EACH BUTTON---####
def selectFasta(self):
filed = QtWidgets.QFileDialog()
myFile = QtWidgets.QFileDialog.getOpenFileName(filed, "Choose a File")
if (myFile[0] != ""):
if not myFile[0].endswith(".fa") and not myFile[0].endswith(
".fna") and not myFile[0].endswith(
".gbff") and not myFile[0].endswith(".fasta"):
QtWidgets.QMessageBox.question(
self, "File Selection Error",
"You have selected an incorrect type of file. "
"Please choose a genbank, fasta, gbff, or a fna file.",
QtWidgets.QMessageBox.Ok)
return
else:
self.nameFile.setText(myFile[0])
self.file = myFile[0]
"""cdir = self.lineEdit.text()
os.chdir(mydir)
self.gdirectory = mydir
print(mydir)
print(cdir)"""
# this function figures out which type of file the user is searching for, and then shows the
# ncbi_search_dialog window
# connected to the button: self.NCBI_File_Search
def prep_ncbi_search(self):
GlobalSettings.mainWindow.ncbi_search_dialog.searchProgressBar.setValue(
0)
GlobalSettings.mainWindow.ncbi_search_dialog.organismLineEdit.setText(
self.lineEdit_1.displayText())
GlobalSettings.mainWindow.ncbi_search_dialog.show()
def submit(self):
warning = ""
if len(self.lineEdit_1.text()) == 0:
warning = warning + "\nYou need to include the organism's name."
if len(self.file) == 0:
warning = warning + "\nYou need to select a file."
if len(warning) != 0:
QtWidgets.QMessageBox.information(self, "Required Information",
warning,
QtWidgets.QMessageBox.Ok)
return
if len(self.lineEdit_2.text()) == 0:
warning = warning + "\nIt is recommended to include the organism's subspecies/strain."
if len(self.lineEdit_3.text()) == 0:
warning = warning + "\nYou must include an organism code (KEGG code recommended)."
if len(warning) != 0:
hold = QtWidgets.QMessageBox.question(
self, "Missing Information", warning +
"\n\nDo you wish to continue without including this information?",
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.No)
if hold == QtWidgets.QMessageBox.No:
return
myjob = CasperJob(
self.lineEdit_1.text() + " " + self.lineEdit_2.text(),
self.lineEdit_2.text(),
self.Endos[self.comboBoxEndo.currentText()],
self.lineEdit_3.text(), self.file, self.tot_len_box.text(),
self.seed_len_box.text(), self.pamBox.isChecked())
self.JobsQueue.append(myjob)
nxtLine = ""
if len(self.JobsQueueBox.toPlainText()) != 0:
nxtLine = "\n"
self.JobsQueueBox.setPlainText(self.JobsQueueBox.toPlainText() +
nxtLine + myjob.name)
def fillEndo(self):
if GlobalSettings.OPERATING_SYSTEM_ID == "Windows":
f = open(self.info_path + "\\CASPERinfo")
else:
f = open(self.info_path + "/CASPERinfo")
while True:
line = f.readline()
if line.startswith('ENDONUCLEASES'):
while True:
line = f.readline()
if (line[0] == "-"):
break
line_tokened = line.split(";")
endo = line_tokened[0]
# Checking to see if there is more than one pam sequence in the list
if line_tokened[1].find(",") != -1:
p_pam = line_tokened[1].split(",")[0]
else:
p_pam = line_tokened[1]
default_seed_length = line_tokened[2]
default_tot_length = line_tokened[3]
self.Endos[endo + "PAM: " + p_pam] = (endo, p_pam,
default_seed_length,
default_tot_length)
break
f.close()
self.comboBoxEndo.addItems(self.Endos.keys())
def endo_settings(self):
# check the if it's 3' or 5', and check the box accordingly
if int(self.seqTrans.endo_info[self.Endos[
self.comboBoxEndo.currentText()][0]][3]) == 3:
self.pamBox.setChecked(0)
elif int(self.seqTrans.endo_info[self.Endos[
self.comboBoxEndo.currentText()][0]][3]) == 5:
self.pamBox.setChecked(1)
self.tot_len_box.setText(
self.Endos[self.comboBoxEndo.currentText()][3])
self.seed_len_box.setText(
self.Endos[self.comboBoxEndo.currentText()][2])
def findFasta(self):
choice = QtWidgets.QMessageBox.question(
self, "Extract!", "Are you sure you want to Quit?",
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
if choice == QtWidgets.QMessageBox.Yes:
sys.exit()
else:
pass
def testcheckandradio(self, state):
if state == QtCore.Qt.Checked:
pass
def whatsthisclicked(self):
QtWidgets.QMessageBox.information(
self, "Organism Code",
"The organism code is the manner in which CASPER will"
" label its data files and references for the organism"
" you are importing here. It is HIGHLY RECOMMENDED that"
" you use the 3-4 letter code used by KEGG as this will"
" aid in automatic accession of annotations from the"
" database.", QtWidgets.QMessageBox.Ok)
def updatekegglist(self):
if len(self.lineEdit_1.text()) == 0:
QtWidgets.QMessageBox.question(
self, "Error!",
"Please enter an organism into the Organism Name!",
QtWidgets.QMessageBox.Ok)
return
self.keggSuggested.clear()
kegg_orglist = self.k.lookfor_organism(self.lineEdit_1.text())
holder = 0
self.keggSuggested.setColumnCount(2)
for item in kegg_orglist:
second_space = item[item.find(" ") + 1:].find(" ") + item.find(" ")
code = item[item.find(" ") + 1:second_space + 1]
item = item[second_space + 2:]
semi = item.find(";")
index = 1
while True:
if item[semi - index] == " ":
break
index = index + 1
organism = item[:semi - index]
self.keggSuggested.setRowCount(holder + 1)
table_code = QtWidgets.QTableWidgetItem(code)
table_organism = QtWidgets.QTableWidgetItem(organism)
self.keggSuggested.setItem(holder, 0, table_organism)
self.keggSuggested.setItem(holder, 1, table_code)
# self.keggsearchresults.insertPlainText(item)
holder += 1
self.keggSuggested.resizeColumnsToContents()
def run_jobs(self):
self.progressBar.setValue(0)
def output_stdout(p):
line = str(p.readAll())
line = line[2:]
line = line[:len(line) - 1]
for lines in filter(None, line.split(r'\r\n')):
if (lines == 'Finished reading in the genome file.'):
self.num_chromo_next = True
elif (self.num_chromo_next == True):
self.num_chromo_next = False
self.num_chromo = int(lines)
elif (lines.find('Chromosome') != -1
and lines.find('complete.') != -1):
temp = lines
temp = temp.replace('Chromosome ', '')
temp = temp.replace(' complete.', '')
if (int(temp) == self.num_chromo):
self.progressBar.setValue(99)
else:
self.progressBar.setValue(
int(temp) / self.num_chromo * 100)
elif (lines == 'Finished Creating File.'):
self.progressBar.setValue(100)
self.output_browser.append(lines)
# Top layer for loop to go through all of the jobs in the queue:
job = self.JobsQueue[0]
program = '"' + GlobalSettings.appdir + '\\Casper_Seq_Finder_Windows" '
self.JobInProgress.setText(job.name)
self.process.readyReadStandardOutput.connect(
partial(output_stdout, self.process))
self.process.start(program, job.get_arguments())
self.JobsQueueBox.clear()
for jobs in self.JobsQueue:
if (job.name != jobs.name):
self.JobsQueueBox.append(jobs.name)
def upon_process_finishing(self):
self.CompletedJobs.append(self.JobsQueue[0].name)
self.JobsQueue.pop(0)
self.process.close()
self.num_chromo = 0
if len(self.JobsQueue) != 0:
self.progressBar.setValue(0)
self.run_jobs()
else:
self.JobInProgress.clear()
self.JobsQueue = []
self.JobsQueueBox.clear()
self.output_browser.clear()
def clear_job_queue(self):
self.process.kill()
self.JobsQueue = []
self.JobsQueueBox.clear()
self.lineEdit_1.clear()
self.lineEdit_2.clear()
self.lineEdit_3.clear()
self.keggSuggested.setRowCount(0)
self.output_browser.clear()
self.JobInProgress.clear()
self.CompletedJobs.clear()
self.nameFile.setText("Name Of File")
self.progressBar.setValue(0)
self.first = False
def reset(self):
self.lineEdit_1.clear()
self.lineEdit_2.clear()
self.lineEdit_3.clear()
self.keggSuggested.clear()
self.first = False
self.nameFile.setText("Name Of File")
def closeEvent(self, event):
# make sure that there are cspr files in the DB
file_names = os.listdir(GlobalSettings.CSPR_DB)
noCSPRFiles = True
for file in file_names:
if 'cspr' in file:
noCSPRFiles = False
break
if noCSPRFiles == True:
error = QtWidgets.QMessageBox.question(
self, "No CSPR File generated",
"No CSPR file has been generate, thus the main program cannot run. Please create a CSPR file."
"Alternatively, you could quit the program. Would you like to quit?",
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.No)
if (error == QtWidgets.QMessageBox.No):
event.ignore()
return
else:
self.close()
else:
self.process.kill()
self.JobsQueue = []
self.JobsQueueBox.clear()
self.lineEdit_1.clear()
self.lineEdit_2.clear()
self.lineEdit_3.clear()
self.keggSuggested.setRowCount(0)
self.output_browser.clear()
self.JobInProgress.clear()
self.CompletedJobs.clear()
self.nameFile.setText("Name Of File")
self.progressBar.setValue(0)
self.first = False
GlobalSettings.CASPER_FOLDER_LOCATION = self.info_path
GlobalSettings.mainWindow.show()
GlobalSettings.mainWindow.getData()
GlobalSettings.MTWin.launch(GlobalSettings.CSPR_DB)
GlobalSettings.pop_Analysis.launch(GlobalSettings.CSPR_DB)
event.accept()
def continue_to_main(self):
# make sure that there are cspr files in the DB
file_names = os.listdir(GlobalSettings.CSPR_DB)
noCSPRFiles = True
for file in file_names:
if 'cspr' in file:
noCSPRFiles = False
break
if noCSPRFiles == True:
error = QtWidgets.QMessageBox.question(
self, "No CSPR File generated",
"No CSPR file has been generate, thus the main program cannot run. Please create a CSPR file."
"Alternatively, you could quit the program. Would you like to quit?",
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.No)
if (error == QtWidgets.QMessageBox.No):
return
else:
self.close()
else:
self.process.kill()
self.JobsQueue = []
self.JobsQueueBox.clear()
self.lineEdit_1.clear()
self.lineEdit_2.clear()
self.lineEdit_3.clear()
self.keggSuggested.setRowCount(0)
self.output_browser.clear()
self.JobInProgress.clear()
self.CompletedJobs.clear()
self.nameFile.setText("Name Of File")
self.progressBar.setValue(0)
self.first = False
GlobalSettings.CASPER_FOLDER_LOCATION = self.info_path
GlobalSettings.mainWindow.show()
GlobalSettings.mainWindow.getData()
GlobalSettings.MTWin.launch(GlobalSettings.CSPR_DB)
GlobalSettings.pop_Analysis.launch(GlobalSettings.CSPR_DB)
self.close()