def createVisualisation(self):
try:
CirGoFileConversion.ConvertToThreeCoulmnsInput(self.inputFileName)
except:
self.statusBar.setMessage("File could not be converted. Please check the file format and it's content!")
traceback.print_exc()
else:
try:
ifn, ife = os.path.splitext(self.inputFileName)
CirGOVisualGO.CircularVisualGO(ifn + "_converted.csv", int(self.nrCategories.get()), float(self.fontSize.get()), self.figureLegendEntry.get(), self.outputFileName) ########### Propoer file naming
except:
self.statusBar.setMessage("File could not be visualised!")
traceback.print_exc()
def main(argv):
print(argv)
argsparser = argparse.ArgumentParser(
prog="CirGO",
usage=
'This is the command line interface for the CirGO visualisation software.\n'
+ '\n HELP: help for using the software. python CirGO.py -h\n' +
'\n GUI: usage for the graphical user interface option of the CirGO software. python CirGO.py -gui\n'
+
'\n COMMAND LINE (CMD): usage for the command line option of the CirGO software. python CirGO.py - inputFile INPUTFILE [-outputFile OUTPUTFILE] [-fontSize FONTSIZE] [-numCat NRCATEGORIES] [-leg FIGURE_LEGEND]\n'
+
'\n INTERACTIVE MODE (INT): interactive option of the CirGO software. python CirGO.py -int\n ',
formatter_class=RawTextHelpFormatter,
epilog=
"Copyright (C) 2018. This software is licensed under the terms of the GNU general public license (version 3).\nIf you use this software, please cite the following publication: ......."
)
arg_group_dummy = argsparser.add_argument_group(
'',
'--------------------------------------------------------------------------------------------------------------------'
)
arg_group_gui = argsparser.add_argument_group(
'GUI',
'Graphical User Interface (GUI) option of the CirGO software.\nExample: python CirGO.py -gui'
)
arg_group_gui.add_argument(
"-gui",
action='store_true',
help=
"GUI option of the CirGO software. If this option is selected, all other command line parameters will be ignored.\n"
)
arg_group_gui.add_argument(" ", action='store_true')
arg_group_cmd = argsparser.add_argument_group(
'CMD',
'Command line option of the CirGO software. \nExample: python CirGO.py -inputFile C:\\mydir\Example_REVIGO_Input_BP.csv -outputFile C:\\mydir\\Visual_BP.svg -fontSize 6.5 -numCat 40 -legend "Name & Proportion of Biological process (inner ring)"'
)
arg_group_cmd.add_argument(
"-inputFile",
default=None,
type=str,
help=
"[csv] Input path and filename of a REVIGO file. \nExample: C:\\mydir\\Example_REVIGO_Input_BP.csv"
)
arg_group_cmd.add_argument(
"-outputFile",
default=None,
type=str,
help=
"[svg] Output path and filename. \nExample: C:\\mydir\\Visual_BP.svg")
arg_group_cmd.add_argument(
'-fontSize',
type=float,
default=DEFAULT_FONT_SIZE,
help="[float] Font Size (Default: " + str(DEFAULT_FONT_SIZE) +
"). Select one from the range 6.0 -7.5 \nExample: 6.5")
arg_group_cmd.add_argument(
'-numCat',
type=int,
default=DEFAULT_NUM_OF_CATEGORIES,
help="[int] Number of Categories to be visualised. (Default: " +
str(DEFAULT_NUM_OF_CATEGORIES) + "). \nExample: 60 or lower")
arg_group_cmd.add_argument(
'-legend',
type=str,
default=DEFAULT_LEGEND_NAME,
help=
"[str] Legend title to be displayed in the figure. Select relevant example of the legend name. \nExample:\n (1) Name & Proportion of Biological process (inner ring)\n (2) Name & Proportion of Cellular component (inner ring)\n (3) Name & Proportion of Molecular function (inner ring) "
)
arg_group_cmd.add_argument(" ", action='store_true')
arg_group_int = argsparser.add_argument_group(
'INT',
'Interactive option of the CirGO software. \nExample: python CirGO.py -int\n'
)
arg_group_int.add_argument(
"-int",
action='store_true',
help=
"Interactive option of the CirGO software. \nInput file from REVIGO as CSV [str]: 'C://mydir/Example_REVIGO_Input_BP.csv' ***NOTE*** provide a file directory as a string, where a backslash '\\' has to be changed to the forward slash '/'.\n \nFont Size (Example - 7.0) [float]: 7.0\n \nNumber of Categories (Example - 40) [int]: 40\n \nLegend name. Example: 'Name & Proportion of Biological process (inner ring)' [str]: 'Name & Proportion of Biological process (inner ring)' ***NOTE*** Select relevant example of the legend name.\n \nOutput file in svg format (Example: input filename + svg) [str]: 'C://mydir/Visual_BP.svg' ***NOTE*** provide a file directory as a string, where a backslash '\\' has to be changed to the forward slash '/'.\n "
)
args = argsparser.parse_args()
# validate arguments
if (args.fontSize <= 1) or (args.numCat < 1):
print(
"Wrong command line parameters: fontSize must be a positive float value, and numCat must be an positive integer value!"
)
sys.exit()
try:
args.fontSize = float(args.fontSize)
args.numCat = int(args.numCat)
except:
print(
"Wrong command line parameters: fontSize must be a positive float value, and numCat must be an positive integer value!"
)
traceback.print_exc()
sys.exit()
if (not args.gui) and (args.inputFile == None) and (not args.int):
print(
"To see a help page, python CirGO.py -h. Otherwise select the GUI, command line or interactive mode of the software!"
)
traceback.print_exc()
sys.exit()
if args.gui:
root = Tk()
app = Application(master=root)
app.master.title('CirGO - Circular Gene Ontology terms Visualisation')
app.mainloop()
root.destroy()
elif args.int:
# Input File --------------------------------------------------------------------------------------------------------------------
infl = input("Input file from REVIGO as CSV [str]: ")
if type(infl) != str:
print(
"Wrong command line parameters: Input File must be a string.")
sys.exit()
try:
infl = str(infl)
except:
print(
'Input file is not a string. Please enter a valid filename as a string.'
)
traceback.print_exc()
sys.exit()
# Font Size --------------------------------------------------------------------------------------------------------------------
insize = raw_input("Font Size (Example - 7.0) [float]: ")
if insize == "":
print("Default Font Size is used. [Example: 7.0]")
insize = DEFAULT_FONT_SIZE
elif type(float(insize)) != float:
print(
"Wrong command line parameters: Font Size must be a positive float value"
)
sys.exit()
elif float(insize) < 0:
print(
"Wrong command line parameters: Font Size must be a positive float value"
)
sys.exit()
try:
insize = float(insize)
except:
print(
"Font Size is not a float. Please enter Font Size as a float.")
traceback.print_exc()
sys.exit()
# Number of Categories--------------------------------------------------------------------------------------------------------------------
incat = raw_input(
"Number of Categories (Example - 40) [int]: ") # a string
if incat == "":
print("Default Number of Categories is used [Example: 40]")
incat = DEFAULT_NUM_OF_CATEGORIES
elif type(int(float(incat))) != int:
print(
"Wrong command line parameters: Number of Categories must be a positive integer value"
)
sys.exit()
elif int(float(incat)) < 0:
print(
"Wrong command line parameters: Number of Categories must be a positive integer value"
)
sys.exit()
try:
incat = int(float(incat))
except:
print(
"Number of Categories is not an integer. Please enter a valid number as an integer."
)
traceback.print_exc()
sys.exit()
# Legend--------------------------------------------------------------------------------------------------------------------
inleg = raw_input(
'Legend name. Example: "Name & Proportion of Biological process (inner ring)" [str]: '
)
if inleg == "":
print(
'Default Legend Name is used [Example: "Name & Proportion of Biological process (inner ring)"]'
)
inleg = DEFAULT_LEGEND_NAME
elif type(inleg) != str:
print(
"Wrong command line parameters: Legend name must be a string.")
sys.exit()
try:
inleg = str(inleg)
except:
print(
"Legen Name is not a string. Please enter a valid Legend Name as a string."
)
traceback.print_exc()
sys.exit()
# OutputFile--------------------------------------------------------------------------------------------------------------------
outfl = input(
"Output file in svg format (Example: input filename + svg) [str]: "
)
if type(outfl) != str:
print(
"Wrong command line parameters: Output file must be a string.")
sys.exit()
try:
outfl = str(outfl)
except:
print(
"Output file is not a string. Please enter a valid filename as a string."
)
traceback.print_exc()
sys.exit()
CirGoFileConversion.ConvertToThreeCoulmnsInput(infl,
infl + "_converted.csv")
CirGOVisualGO.CircularVisualGO(infl + "_converted.csv", int(incat),
float(insize), str(inleg), str(outfl))
else:
try:
if os.path.isfile(args.inputFile):
print("Opening input file: " + args.inputFile)
fn, fe = os.path.splitext(args.inputFile)
if (args.outputFile == None):
args.outputFile = fn + ".svg"
CirGoFileConversion.ConvertToThreeCoulmnsInput(
args.inputFile, fn + "_converted.csv")
else:
print(
"Input file could not be found. Please enter a valid filename."
)
sys.exit()
except:
print(
"File could not be converted. Please check if the file exists and if the file format is correct!"
)
traceback.print_exc()
sys.exit()
try:
fn, fe = os.path.splitext(args.inputFile)
CirGOVisualGO.CircularVisualGO(fn + "_converted.csv",
int(args.numCat),
float(args.fontSize), args.legend,
args.outputFile)
except:
traceback.print_exc()
print("File could not be visualised!")
sys.exit()