def scriptSM():
screen.clear()
screen.border(0)
screen.addstr(2, 2, "This is Motif Search")
screen.addstr(4, 4, "Please enter a input file for Motif Search")
screen.addstr(7, 4, "Please name the first output file (WCFS1_glc1)")
screen.addstr(10, 4, "Please name the second output file (NC8_glc1)")
screen.addstr(13, 4, "Please name the third output file (WCFS1_glc2)")
screen.addstr(16, 4, "Please name the last output file (NC8_glc2)")
screen.refresh()
thirdClass = class3()
userInput = screen.getstr(5, 10, 60)
userOutput = screen.getstr(8, 10, 60)
userOutput2 = screen.getstr(11, 10, 60)
userOutput3 = screen.getstr(14, 10, 60)
userOutput4 = screen.getstr(17, 10, 60)
try:
thirdClass.motifSearch(userInput, userOutput, userOutput2, userOutput3, userOutput4)
screen.clear()
screen.border(0)
screen.addstr(2, 4, "Motif Search succes!")
screen.refresh()
time.sleep(3)
except:
curses.flash()
show_error("Invalid file name. Try again.")
screen.addstr(2, 2, "0% complete...")
screen.refresh()
time.sleep(1)
firstClass.filterLPs(userInput, userOutput)
screen.clear()
screen.border(0)
screen.addstr(2, 2, "25% complete...")
screen.refresh()
secondClass = class2()
userOutput2 = "FO_output"
secondClass.zoekOrthologen(userOutput+".txt", userOutput2)
screen.clear()
screen.border(0)
screen.addstr(2, 2, "50% complete...")
screen.refresh()
thirdClass = class3()
userOutput3 = "MS_output_WCFS1_glc1"
userOutput4 = "MS_output_NC8_glc1"
userOutput5 = "MS_output_WCFS1_glc2"
userOutput6 = "MS_output_NC8_glc2"
thirdClass.motifSearch(userOutput2+".txt", userOutput3, userOutput4, userOutput5, userOutput6)
screen.clear()
screen.border(0)
screen.addstr(2, 2, "75% complete...")
screen.refresh()
fourthClass = class4()
Parameters = "-dna -nmotifs 1 -minw 20 -maxw 50 -mod zoops -minsites 150 -maxsites 745"
fourthClass.callMEME(userOutput3+".txt", MEMEpath, Parameters)
fourthClass.callMEME(userOutput4+".txt", MEMEpath, Parameters)
fourthClass.callMEME(userOutput5+".txt", MEMEpath, Parameters)
fourthClass.callMEME(userOutput6+".txt", MEMEpath, Parameters)