add both dmso and formamide additives, update readme

README.md

@@ -1,9 +1,9 @@
 # tm_calculator_gui
 Calculates the melting temperature of a user imported  forward and reverse primer based on the SantaLucia, 1998 salt correction formula used also in primer3 and primer blast. It can correct the tm calculation based on the existence of additives formamide & DMSO.
 ## Windows and ubuntu linux GUI stadalone programs
-GUI executables are avaliable in: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7977708.svg)](https://doi.org/10.5281/zenodo.7977708)  
+GUI executables are avaliable in: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7978091.svg)](https://doi.org/10.5281/zenodo.7978091)
 ## Citation
-Olga Tsiouri. (2023). Tm calculator GUI: Windows and ubuntu linux GUI apps that calculate the melting temperature of a user imported  forward and reverse primer based on primer blast default parameters. Zenodo. https://doi.org/10.5281/zenodo.7977708
+Olga Tsiouri. (2023). Tm calculator GUI: Windows and ubuntu linux GUI apps that calculate the melting temperature of a user imported  forward and reverse primer based on primer blast default parameters. Zenodo. https://doi.org/10.5281/zenodo.7978091
 ## Depedences
 1. python3.10
 2. anaconda/miniconda

tm_calculator_gui.py

@@ -3,20 +3,20 @@
 from Bio.SeqUtils import MeltingTemp as mt
 from Bio.Seq import Seq
 # imput parameters
-@Gooey(required_cols=2, program_name='Tm calculator(Celsius)', default_size=(700, 740), header_bg_color= '#DCDCDC', terminal_font_color= '#000000', terminal_panel_color= '#DCDCDC',terminal_font_size=14, clear_before_run=True)
+@Gooey(required_cols=2, program_name='Tm calculator(Celsius)', default_size=(740, 740), header_bg_color= '#DCDCDC', terminal_font_color= '#000000', terminal_panel_color= '#DCDCDC',terminal_font_size=20, clear_before_run=True)
 def main():
 	ap = GooeyParser()
-	ap.add_argument("-forward", "--Forward primer", required=True, type=str, help="forward primer sequence")
-	ap.add_argument("-reverse", "--Reverse primer", required=True, type=str, help="reverse primer sequence")
+	ap.add_argument("-forward", "--Forward primer", required=True, type=str, help="Forward primer sequence")
+	ap.add_argument("-reverse", "--Reverse primer", required=True, type=str, help="Reverse primer sequence")
 	ap.add_argument("-Na", "--Na", required=False, type=float, default=50.0, help="Na+ concentration")
 	ap.add_argument("-Mg", "--Mg", required=False, type=float, default=1.5, help="Mg2+ concentration")
 	ap.add_argument("-dNTPs", "--dNTPs", required=False, type=float, default=0.6, help="dNTPs concentration")
-	ap.add_argument("-additive", "--additive", required=False, type=str, default="no", choices=["no","yes"], help="correct Tm calculation based on additive/s concertrations")
-	ap.add_argument("-type", "--additive type", required=False, type=str, default="DMSO", choices=["DMSO","formamide"], help="additive type used")
-	ap.add_argument("-per", "--percentage of DSMO", required=False, type=float, default=2.0, help="%DMSO concertration")
-	ap.add_argument("-decrease", "--decrease of DMSO", required=False, type=float, default=0.65, help="How much should Tm decrease per percent DMSO")
-	ap.add_argument("-conc", "--percentage of formamide", required=False, type=float, default=1.0, help="".join(["%","formamide concertration"]))
-	ap.add_argument("-dec", "--decrease of formamide", required=False, type=float, default=0.65, help="How much should Tm decrease per percent formamide")	
+	ap.add_argument("-additive", "--PCR additive", required=False, type=str, default="no", choices=["no","yes"], help="Correct Tm calculation based on the additive's concertrations")
+	ap.add_argument("-type", "--Additive type", required=False, type=str, default="DMSO", choices=["DMSO","formamide"], help="Additive type used")
+	ap.add_argument("-per", "--Percentage of DSMO", required=False, type=float, default=2.0, help="%DMSO concertration")
+	ap.add_argument("-Decrease", "--Decrease of DMSO", required=False, type=float, default=0.65, help="How much should Tm Decrease per percent DMSO")
+	ap.add_argument("-conc", "--Percentage of formamide", required=False, type=float, default=1.0, help="".join(["%","formamide concertration"]))
+	ap.add_argument("-dec", "--Decrease of formamide", required=False, type=float, default=0.65, help="How much should Tm Decrease per percent formamide")	
 	args = vars(ap.parse_args())
 	# import forward primer
 	frwd = Seq(args['Forward primer'])
@@ -27,23 +27,22 @@ def main():
 	# calculate Tm of reverse primer
 	tmr = round(mt.Tm_NN(rever, Na=args['Na'], Mg=args['Mg'], dNTPs=args['dNTPs']), 2)
 	# if DMSO or formamide is added fix Tm calculation
-	if args['additive'] == "no":
-		print(f'The Tm of the forward primer is: {tmf}') # creates the celsius symbol
+	if args['PCR additive'] == "no":
+		# print to GUI console
+		print(f'The Tm of the forward primer is: {tmf}')
 		print(f'The Tm of the reverse primer is: {tmr}')
 		print(f'The Tm difference between the primers is: {abs(round(tmf-tmr, 2))}') # abs will keep the difference positive
 	else:
-		if args['additive type'] == "DMSO":
-			fixedtmf = round(mt.chem_correction(tmf, DMSO=args['percentage of DSMO'],DMSOfactor=args['decrease of DMSO']) ,2)
-			print(f'The Tm of the forward primer is: {fixedtmf}')
-			fixedtmr = round(mt.chem_correction(tmr, DMSO=args['percentage of DSMO'],DMSOfactor=args['decrease of DMSO']) ,2)
-			print(f'The Tm of the reverse primer is: {fixedtmr}')
-			print(f'The Tm difference between the primers is: {abs(round(fixedtmf-fixedtmr, 2))}') # abs will keep the difference positive
+		if args['Additive type'] == "DMSO":
+			fixedtmf = round(mt.chem_correction(tmf, DMSO=args['Percentage of DSMO'],DMSOfactor=args['Decrease of DMSO']) ,2)
+			fixedtmr = round(mt.chem_correction(tmr, DMSO=args['Percentage of DSMO'],DMSOfactor=args['Decrease of DMSO']) ,2)
 		else:
-			fixedtmf = round(mt.chem_correction(tmf, fmd=args['percentage of formamide'],fmdfactor=args['decrease of formamide']) ,2)
-			print(f'The Tm of the forward primer is: {fixedtmf}')
-			fixedtmr = round(mt.chem_correction(tmr, fmd=args['percentage of formamide'],fmdfactor=args['decrease of formamide']) ,2)
-			print(f'The Tm of the reverse primer is: {fixedtmr}')
-			print(f'The Tm difference between the primers is: {abs(round(fixedtmf-fixedtmr, 2))}') # abs will keep the difference positive
+			fixedtmf = round(mt.chem_correction(tmf, fmd=args['Percentage of formamide'],fmdfactor=args['Decrease of formamide']) ,2)
+			fixedtmr = round(mt.chem_correction(tmr, fmd=args['Percentage of formamide'],fmdfactor=args['Decrease of formamide']) ,2)
+		# print to GUI console
+		print(f'The Tm of the forward primer is: {fixedtmf}')
+		print(f'The Tm of the reverse primer is: {fixedtmr}')
+		print(f'The Tm difference between the primers is: {abs(round(fixedtmf-fixedtmr, 2))}') # abs will keep the difference positive
 
 if __name__ == '__main__':
 	main()