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src/Phyx_Gui.py deleted 100644 → 0
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import Tkinter,os,sys
from Tkinter import *
class GUI:
def __init__(self, master):
self.master = master
master.title("PHYX GUI")
self.label = Label(master, text="Path to -a").grid(row=0,column=0)
#self.label.pack()
global a
a = Tkinter.StringVar()
self.a_seq = Entry(master, bd=5, textvariable=a).grid(row=0,column=1)
#self.aa_seq.pack(side = LEFT)
self.label = Label(master, text="Path to -b").grid(row=0,column=2)
#self.label.pack(side = LEFT)
global b
b = Tkinter.StringVar()
self.b_seq = Entry(master, bd=5, textvariable=b).grid(row=0,column=3)
#self.b_seq.pack(side = LEFT)
self.label = Label(master, text="Path to -c").grid(row=0,column=4)
#self.label.pack(side = LEFT)
global c
c = Tkinter.StringVar()
self.c_seq = Entry(master, bd=5, textvariable=c).grid(row=0,column=5)
#self.c_seq.pack(side = LEFT)
self.label = Label(master, text="Path to -d").grid(row=0,column=6)
#self.label.pack(side = LEFT)
global d
d = Tkinter.StringVar()
self.d_seq = Entry(master, bd=5, textvariable=d).grid(row=0,column=7)
#self.d_seq.pack(side = LEFT)
self.label = Label(master, text="Path to -e").grid(row=1,column=0)
global e
e = Tkinter.StringVar()
self.e_seq = Entry(master, bd=5, textvariable=e).grid(row=1,column=1)
self.label = Label(master, text="Path to -f").grid(row=1,column=2)
global f
f = Tkinter.StringVar()
self.f_seq = Entry(master, bd=5, textvariable=f).grid(row=1,column=3)
self.label = Label(master, text="Path to -g").grid(row=1,column=4)
global g
g = Tkinter.StringVar()
self.g_seq = Entry(master, bd=5, textvariable=g).grid(row=1,column=5)
self.label = Label(master, text="Path to -h").grid(row=1,column=6)
global h
h = Tkinter.StringVar()
self.h_seq = Entry(master, bd=5, textvariable=h).grid(row=1,column=7)
self.label = Label(master, text="Path to -i").grid(row=2,column=0)
global i
i = Tkinter.StringVar()
self.i_seq = Entry(master, bd=5, textvariable=i).grid(row=2,column=1)
self.label = Label(master, text="Path to -j").grid(row=2,column=2)
global j
j = Tkinter.StringVar()
self.j_seq = Entry(master, bd=5, textvariable=j).grid(row=2,column=3)
self.label = Label(master, text="Path to -k").grid(row=2,column=4)
global k
k = Tkinter.StringVar()
self.k_seq = Entry(master, bd=5, textvariable=k).grid(row=2,column=5)
self.label = Label(master, text="Path to -l").grid(row=2,column=6)
global l
l = Tkinter.StringVar()
self.l_seq = Entry(master, bd=5, textvariable=l).grid(row=2,column=7)
self.label = Label(master, text="Path to -m").grid(row=3,column=0)
global m
m = Tkinter.StringVar()
self.m_seq = Entry(master, bd=5, textvariable=m).grid(row=3,column=1)
self.label = Label(master, text="Path to -n").grid(row=3,column=2)
global n
n = Tkinter.StringVar()
self.n_seq = Entry(master, bd=5, textvariable=n).grid(row=3,column=3)
self.label = Label(master, text="Path to -o").grid(row=3,column=4)
global o
o = Tkinter.StringVar()
self.o_seq = Entry(master, bd=5, textvariable=o).grid(row=3,column=5)
self.label = Label(master, text="Path to -p").grid(row=3,column=6)
global p
p = Tkinter.StringVar()
self.p_seq = Entry(master, bd=5, textvariable=p).grid(row=3,column=7)
self.label = Label(master, text="Path to -q").grid(row=4,column=0)
global q
q = Tkinter.StringVar()
self.q_seq = Entry(master, bd=5, textvariable=q).grid(row=4,column=1)
self.label = Label(master, text="Path to -r").grid(row=4,column=2)
global r
r = Tkinter.StringVar()
self.r_seq = Entry(master, bd=5, textvariable=r).grid(row=4,column=3)
self.label = Label(master, text="Path to -s").grid(row=4,column=4)
global s
s = Tkinter.StringVar()
self.s_seq = Entry(master, bd=5, textvariable=s).grid(row=4,column=5)
self.label = Label(master, text="Path to -t").grid(row=4,column=6)
global t
t = Tkinter.StringVar()
self.t_seq = Entry(master, bd=5, textvariable=t).grid(row=4,column=7)
self.label = Label(master, text="Path to -u").grid(row=5,column=0)
global u
u = Tkinter.StringVar()
self.u_seq = Entry(master, bd=5, textvariable=u).grid(row=5,column=1)
self.label = Label(master, text="Path to -v").grid(row=5,column=2)
global v
v = Tkinter.StringVar()
self.v_seq = Entry(master, bd=5, textvariable=v).grid(row=5,column=3)
self.label = Label(master, text="Path to -w").grid(row=5,column=4)
global w
w = Tkinter.StringVar()
self.w_seq = Entry(master, bd=5, textvariable=w).grid(row=5,column=5)
self.label = Label(master, text="Path to -x").grid(row=5,column=6)
global x
x = Tkinter.StringVar()
self.x_seq = Entry(master, bd=5, textvariable=x).grid(row=5,column=7)
self.label = Label(master, text="Path to -y").grid(row=6,column=0)
global y
y = Tkinter.StringVar()
self.y_seq = Entry(master, bd=5, textvariable=y).grid(row=6,column=1)
self.label = Label(master, text="Path to -z").grid(row=6,column=2)
global z
z = Tkinter.StringVar()
self.z_seq = Entry(master, bd=5, textvariable=z).grid(row=6,column=3)
"""
self.label = Label(master, text="Path to -n")
self.label.pack(padx=10)
global test2
test2 = Tkinter.StringVar()
self.nuc_seq = Entry(master, bd=5, textvariable=test2)
self.nuc_seq.pack(padx=10)
self.label = Label(master, text="Outfile -o")
self.label.pack()
global test3
test3 = ""
test3 = Tkinter.StringVar()
self.out_seq = Entry(master, bd=5, textvariable=test3)
self.out_seq.pack()
self.label = Label(master, text="help -h")
self.label.pack()
global help_me
help_me = ""
help_me = Tkinter.StringVar()
self.help_seq = Entry(master, bd=5, textvariable=help_me)
self.help_seq.pack()
"""
self.aa_button = Button(master, text="Run pxaatocdn", command=self.aa).grid(row=7,column=0)
#self.aa_button.pack()
self.bdfit_button = Button(master, text="Run pxbdfit", command=self.bdfit).grid(row=7,column=1)
self.bdsim_button = Button(master, text="Run pxbdsim", command=self.bdsim).grid(row=7,column=2)
self.boot_button = Button(master, text="Run pxboot", command=self.boot).grid(row=7,column=3)
self.bp_button = Button(master, text="Run pxbp", command=self.bp).grid(row=7,column=4)
self.bpseq_button = Button(master, text="Run pxbpseq", command=self.bpseq).grid(row=7,column=5)
self.cat_button = Button(master, text="Run pxcat", command=self.cat).grid(row=7,column=6)
self.clsq_button = Button(master, text="Run pxclsq", command=self.clsq).grid(row=7,column=7)
self.conseq_button = Button(master, text="Run pxconseq", command=self.conseq).grid(row=8,column=0)
self.contrates_button = Button(master, text="Run pxcontrates", command=self.contrates).grid(row=8,column=1)
self.fqfilt_button = Button(master, text="Run pxfqfilt", command=self.fqfilt).grid(row=8,column=2)
self.lsseq_button = Button(master, text="Run pxlsseq", command=self.lsseq).grid(row=8,column=3)
self.lstr_button = Button(master, text="Run pxlstr", command=self.lstr).grid(row=8,column=4)
self.mrca_button = Button(master, text="Run pxmrca", command=self.mrca).grid(row=8,column=5)
self.mrcacut_button = Button(master, text="Run pxmrcacut", command=self.mrcacut).grid(row=8,column=6)
self.mrcaname_button = Button(master, text="Run pxmrcaname", command=self.mrcaname).grid(row=8,column=7)
self.nj_button = Button(master, text="Run pxnj", command=self.nj).grid(row=9,column=0)
self.nni_button = Button(master, text="Run pxnni", command=self.nni).grid(row=9,column=1)
self.nw_button = Button(master, text="Run pxnw", command=self.nw).grid(row=9,column=2)
self.recode_button = Button(master, text="Run pxrecode", command=self.recode).grid(row=9,column=3)
self.revcomp_button = Button(master, text="Run pxrevcomp", command=self.revcomp).grid(row=9,column=4)
self.rms_button = Button(master, text="Run pxrms", command=self.rms).grid(row=9,column=5)
self.rmt_button = Button(master, text="Run pxrmt", command=self.rmt).grid(row=9,column=6)
self.rr_button = Button(master, text="Run pxrr", command=self.rr).grid(row=9,column=7)
self.seqgen_button = Button(master, text="Run pxseqgen", command=self.seqgen).grid(row=10,column=0)
self.stofa_button = Button(master, text="Run pxstofa", command=self.stofa).grid(row=10,column=1)
self.stonex_button = Button(master, text="Run pxstonex", command=self.stonex).grid(row=10,column=2)
self.stophy_button = Button(master, text="Run pxstophy", command=self.stophy).grid(row=10,column=3)
self.strec_button = Button(master, text="Run pxstrec", command=self.strec).grid(row=10,column=4)
self.sw_button = Button(master, text="Run pxsw", command=self.sw).grid(row=10,column=5)
self.tlate_button = Button(master, text="Run pxtlate", command=self.tlate).grid(row=10,column=6)
self.upgma_button = Button(master, text="Run pxupgma", command=self.upgma).grid(row=10,column=7)
#self.seqgen_button.pack()
self.h_button = Button(master, text="print help menu", command=self.h).grid(row=11,column=3)
#self.h_button.pack()
#global help_on
#help_on = ""
#help_on = Tkinter.StringVar()
self.close_button = Button(master, text="Close program", command=master.quit).grid(row=11,column=4)
#self.close_button.pack()
def aa(self):
if (h.get() != ""):
cmd = "pxaatocdn -h"
else:
cmd = "pxaatocdn -a " + a.get() + " -n " + n.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def bdfit(self):
if (h.get() != ""):
cmd = "pxbdfit -h"
else:
cmd = "pxbdfit -t " + t.get()
if (m.get() != ""):
cmd += " -m " + m.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def bdsim(self):
if (h.get() != ""):
cmd = "pxbdsim -h"
else:
cmd = "pxbdsim "
if (e.get() != ""):
cmd += " -e " + e.get()
if (t.get() != ""):
cmd += " -t " + t.get()
if (b.get() != ""):
cmd += " -b " + b.get()
if (d.get() != ""):
cmd += " -d " + d.get()
if (n.get() != ""):
cmd += " -n " + n.get()
if (s.get() != ""):
cmd += " -s " + s.get()
if (x.get() != ""):
cmd += " -x " + x.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def boot(self):
if (h.get() != ""):
cmd = "pxboot -h"
else:
cmd = "pxboot "
if (s.get() != ""):
cmd += " -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
if (p.get() != ""):
cmd += " -p " + p.get()
if (f.get() != ""):
cmd += " -f " + f.get()
if (x.get() != ""):
cmd += " -x " + x.get()
os.system(cmd)
def bp(self):
if (h.get() != ""):
cmd = "pxbp -h"
else:
cmd = "pxbp -t" + t.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def bpseq(self):
if (h.get() != ""):
cmd = "pxbpseq -h"
else:
cmd = "pxbpseq -t" + t.get() + " -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def cat(self):
if (h.get() != ""):
cmd = "pxcat -h"
else:
cmd = "pxcat -s " + s.get()
if (p.get() != ""):
cmd += " -p " + p.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def clsq(self):
if (h.get() != ""):
cmd = "pxclsq -h"
else:
cmd = "pxclsq -s " + s.get()
if (p.get() != ""):
cmd += " -p " + p.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def conseq(self):
if (h.get() != ""):
cmd = "pxconseq -h"
else:
cmd = "pxconseq -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def contrates(self):
if (h.get() != ""):
cmd = "pxcontrates -h"
else:
cmd = "pxcontrates -s " + s.get()
if (c.get() != ""):
cmd += " -c " + c.get()
if (t.get() != ""):
cmd += " -t " + t.get()
if (a.get() != ""):
cmd += " -a " + a.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def fqfilt(self):
if (h.get() != ""):
cmd = "pxfqfilt -h"
else:
cmd = "pxfqfilt -s " + s.get()
if (m.get() != ""):
cmd += " -m " + m.get()
if (s.get() != ""):
cmd += " -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def lsseq(self):
if (h.get() != ""):
cmd = "pxlsseq -h"
else:
cmd = "pxlsseq -s " + s.get()
if (a.get() != ""):
cmd += " -a "
if (p.get() != ""):
cmd += " -p "
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def lstr(self):
if (h.get() != ""):
cmd = "pxlstr -h"
else:
cmd = "pxlstr -t " + t.get()
if (a.get() != ""):
cmd += " -a "
if (r.get() != ""):
cmd += " -r "
if (b.get() != ""):
cmd += " -b "
if (u.get() != ""):
cmd += " -u "
if (n.get() != ""):
cmd += " -n "
if (l.get() != ""):
cmd += " -l "
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def mrca(self):
if (h.get() != ""):
cmd = "pxmrca -h"
else:
cmd = "pxmrca -t " + t.get()
if (m.get() != ""):
cmd += " -m " + m.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def mrcacut(self):
if (h.get() != ""):
cmd = "pxmrcacut -h"
else:
cmd = "pxmrcacut -t " + t.get()
if (m.get() != ""):
cmd += " -m " + m.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def mrcaname(self):
if (h.get() != ""):
cmd = "pxmrcaname -h"
else:
cmd = "pxmrcaname -t " + t.get()
if (m.get() != ""):
cmd += " -m " + m.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def nj(self):
if (h.get() != ""):
cmd = "pxnj -h"
else:
cmd = "pxnj -s " + s.get()
if (n.get() != ""):
cmd += " -n " + n.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def nni(self):
if (h.get() != ""):
cmd = "pxnni -h"
else:
cmd = "pxnni -t " + t.get()
if (x.get() != ""):
cmd += " -x " + x.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def nw(self):
if (h.get() != ""):
cmd = "pxnw -h"
else:
cmd = "pxnw -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
if (a.get() != ""):
cmd += " -a " + a.get()
if (t.get() != ""):
cmd += " -t " + t.get()
if (m.get() != ""):
cmd += " -m " + m.get()
if (n.get() != ""):
cmd += " -n " + n.get()
if (v.get() != ""):
cmd += " -v " + v.get()
os.system(cmd)
def recode(self):
if (h.get() != ""):
cmd = "pxrecode -h"
else:
cmd = "pxrecode -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def revcomp(self):
if (h.get() != ""):
cmd = "pxrevcomp -h"
else:
cmd = "pxrevcomp -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def rms(self):
if (h.get() != ""):
cmd = "pxrms -h"
else:
cmd = "pxrms -s " + s.get()
if (r.get() != ""):
cmd += " -r " + r.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def rmt(self):
if (h.get() != ""):
cmd = "pxrmt -h"
else:
cmd = "pxrmt -t " + t.get()
if (n.get() != ""):
cmd += " -n " + n.get()
if (f.get() != ""):
cmd += " -f " + f.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def rr(self):
if (h.get() != ""):
cmd = "pxrr -h"
else:
cmd = "pxrr -t " + t.get()
if (f.get() != ""):
cmd += " -f " + f.get()
if (u.get() != ""):
cmd += " -u " + u.get()
if (s.get() != ""):
cmd += " -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def seqgen(self):
if (h.get() != ""):
cmd = "pxseqgen -h"
else:
cmd = "pxseqgen -t " + t.get()
if (o.get() != ""):
cmd += " -o " + o.get()
if (l.get() != ""):
cmd += " -l " + l.get()
if (c.get() != ""):
cmd += " -c "
if (b.get() != ""):
cmd += " -b " + b.get()
if (w.get() != ""):
cmd += " -w " + w.get()
if (q.get() != ""):
cmd += " -q " + q.get()
if (g.get() != ""):
cmd += " -g " + g.get()
if (r.get() != ""):
cmd += " -r " + r.get()
if (n.get() != ""):
cmd += " -n " + n.get()
if (x.get() != ""):
cmd += " -x " + x.get()
if (a.get() != ""):
cmd += " -a "
if (p.get() != ""):
cmd += " -p "
if (m.get() != ""):
cmd += " -m " + m.get()
if (k.get() != ""):
cmd += " -k " + k.get()
os.system(cmd)
def stofa(self):
if (h.get() != ""):
cmd = "pxstofa -h"
else:
cmd = "pxstofa -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def stonex(self):
if (h.get() != ""):
cmd = "pxstonex -h"
else:
cmd = "pxstonex -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def stophy(self):
if (h.get() != ""):
cmd = "pxstophy -h"
else:
cmd = "pxstophy -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def strec(self):
if (h.get() != ""):
cmd = "pxstrec -h"
else:
cmd = "pxstrec -d" + d.get()
if (w.get() != ""):
cmd += " -w "
if (z.get() != ""):
cmd += " -z "
if (t.get() != ""):
cmd += " -t " + t.get()
if (c.get() != ""):
cmd += " -c " + c.get()
if (o.get() != ""):
cmd += " -o " + o.get()
if (n.get() != ""):
cmd += " -n " + n.get()
if (a.get() != ""):
cmd += " -a " + a.get()
if (m.get() != ""):
cmd += " -m " + m.get()
if (p.get() != ""):
cmd += " -p " + p.get()
if (l.get() != ""):
cmd += " -l " + l.get()
os.system(cmd)
def sw(self):
if (h.get() != ""):
cmd = "pxsw -h"
else:
cmd = "pxsw -s" + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
if (a.get() != ""):
cmd += " -a " + a.get()
if (t.get() != ""):
cmd += " -t " + t.get()
if (m.get() != ""):
cmd += " -m " + m.get()
if (n.get() != ""):
cmd += " -n " + n.get()
if (v.get() != ""):
cmd += " -v " + v.get()
os.system(cmd)
def tlate(self):
if (h.get() != ""):
cmd = "pxtlate -h"
else:
cmd = "pxtlate -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def upgma(self):
if (h.get() != ""):
cmd = "pxupgma -h"
else:
cmd = "pxupgma -s " + s.get()
if (o.get() != ""):
cmd += " -o " + o.get()
os.system(cmd)
def h(self):
print "========================================================="
print "This is GUI for PHYX designed to make input easier"
print "Type the location of the file or value into the box"
print "For help on a program, type anything into the help box"
print "and click the program you want help with. Not all options are"
print "needed for all programs so only fill in boxes used for "
print "the program of interest. Anything extra filled in will be"
print "ignored if it is not an option for the program"
print "If the programs option does not require an argument"
print "simply type something into the box and it will activate"
print "that argument"
print "Copyright (C) 2015 FePhyFoFum\nLicense GPLv3\nwritten by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)"
print "========================================================="
root = Tk()
my_gui = GUI(root)
root.mainloop()
src/configure deleted 100755 → 0
View file @ 673e523a
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