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snipsa-gui.py
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snipsa-gui.py
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#!/usr/bin/python3
import sys
import os
import tkinter as tk
import tkinter.filedialog
from tkinter import scrolledtext
import haplomt
import haploy
import haploy_anno_import
bam_support=1
#haploy.use_ftdna_tree = 1
if bam_support:
import bamload
import snpload
def handle_ftdna_select():
f = tkinter.filedialog.askopenfile()
if f:
fname = f.name
else:
return
haploy_anno_import.import_single_ft_project(fname)
def handle_bam_select():
f = tkinter.filedialog.askopenfile()
if f:
bamname = f.name
else:
return
in_build = bamload.get_build(bamname)
bamload.setup_conv(in_build)
snpset = bamload.full_convert(bamname)
snpload.save(bamname+'.snp.txt', snpset, 38)
snpname = bamname+'.snp.txt'
message = 'SNP file written to ' + snpname
scr.config(state=tk.NORMAL)
scr.delete('1.0', tk.END)
scr.insert('1.0', message)
scr.config(state=tk.DISABLED)
scr.see("end")
fnamevar.set(snpname)
def handle_file_select():
f = tkinter.filedialog.askopenfile()
if f:
fname = f.name
else:
return
fnamevar.set(fname)
dbmt_loaded = 0
dby_loaded = 0
def handle_findmt():
global dbmt_loaded
if not dbmt_loaded:
dbmt_loaded = 1
haplomt.load_db()
do_uptree = report_snps.get()
do_all = report_all.get()
force = pathvar.get()
vcf_sample = vcfvar.get().strip()
buildstr = buildvar.get()
force_build=0
if buildstr == 'Build36': force_build = 36
if buildstr == 'Build37': force_build = 37
if buildstr == 'Build38': force_build = 38
fname = fnamevar.get()
print("Reporting file: "+fname)
num = int(numbox.get())
rep = haplomt.report(fname, num, do_uptree=do_uptree, do_extra=do_uptree, do_all=do_all, filt=force, force=force, vcf_sample=vcf_sample, force_build=force_build)
print("Done")
scr.config(state=tk.NORMAL)
scr.delete('1.0', tk.END)
scr.insert('1.0', rep)
scr.config(state=tk.DISABLED)
scr.see("end")
def handle_findy():
global dby_loaded
if not dby_loaded:
dby_loaded = 1
haploy.load_db2j()
haploy.load_annotations('haploy_annodb_*.txt')
do_uptree = report_snps.get()
do_all = report_all.get()
force = pathvar.get()
vcf_sample = vcfvar.get().strip()
buildstr = buildvar.get()
force_build=0
if buildstr == 'Build36': force_build = 36
if buildstr == 'Build37': force_build = 37
if buildstr == 'Build38': force_build = 38
fname = fnamevar.get()
print("Reporting file: "+fname)
num = int(numbox.get())
rep = haploy.report(fname, num, do_uptree=do_uptree, do_extra=do_uptree, do_all=do_all, filt=force, force=force, vcf_sample=vcf_sample, force_build=force_build)
print("Done")
scr.config(state=tk.NORMAL)
scr.delete('1.0', tk.END)
scr.insert('1.0', rep)
scr.config(state=tk.DISABLED)
scr.see("end")
window = tk.Tk()
window.title("Snipsa GUI")
window.geometry("950x700")
window.minsize(600, 300)
hdrframe=tk.Frame(window)
hdrframe.pack(fill='x')
# File
iframe=tk.Frame(hdrframe)
iframe.pack(fill='both')
cbutton4 = tk.Button(iframe, text="Import FTDNA project html", command=handle_ftdna_select)
cbutton4.pack(side=tk.LEFT, fill='x', expand=True)
if bam_support:
cbutton3 = tk.Button(iframe, text="Import BAM", command=handle_bam_select)
cbutton3.pack(side=tk.LEFT, fill='x', expand=True)
# File
fframe=tk.Frame(hdrframe)
fframe.pack(fill='both')
button = tk.Button(fframe, text="Choose file", command=handle_file_select)
button.pack(side=tk.LEFT)
fnamevar = tk.StringVar()
fnamevar.set("No file selected")
fnamelabel=tk.Label(fframe, textvariable=fnamevar, anchor='w')
fnamelabel.pack(side=tk.LEFT, fill='both', expand=True)
vcflabel=tk.Label(fframe, text='VCF sample:', anchor='w')
vcflabel.pack(side=tk.LEFT, fill='both')
vcfvar = tk.StringVar()
vcfbox = tk.Entry(fframe, textvariable=vcfvar,width=10)
vcfbox.pack(side=tk.LEFT)
buildvar = tk.StringVar()
buildchoices = {'Auto', 'Build36', 'Build37', 'Build38'}
buildvar.set('Auto')
builddropdown = tk.OptionMenu(fframe, buildvar, *buildchoices)
builddropdown.pack(side=tk.LEFT)
# Settings
sframe=tk.Frame(hdrframe)
sframe.pack(fill='both')
nbestlabel=tk.Label(sframe, text='Show n best matches:', anchor='w')
nbestlabel.pack(side=tk.LEFT, fill='both')
numbox = tk.Spinbox(sframe,from_=1, to=1000, width=3, text="aaaa")
numbox.pack(side=tk.LEFT)
report_snps = tk.IntVar(value=1)
snplabel=tk.Label(sframe, text='Show path:', anchor='w')
snplabel.pack(side=tk.LEFT, fill='both')
rscbox = tk.Checkbutton(sframe, variable=report_snps)
rscbox.pack(side=tk.LEFT)
report_all = tk.IntVar(value=0)
alllabel=tk.Label(sframe, text='Show all SNPs:', anchor='w')
alllabel.pack(side=tk.LEFT, fill='both')
allbox = tk.Checkbutton(sframe, variable=report_all)
allbox.pack(side=tk.LEFT)
pathlabel=tk.Label(sframe, text='Exact path to:', anchor='w')
pathlabel.pack(side=tk.LEFT, fill='both')
pathvar = tk.StringVar()
pathbox = tk.Entry(sframe, textvariable=pathvar,width=6)
pathbox.pack(side=tk.LEFT)
# Command
cframe=tk.Frame(hdrframe)
cframe.pack()
cbutton1 = tk.Button(cframe, text="Find MT", command=handle_findmt)
cbutton1.pack(side=tk.LEFT, fill='x', expand=True)
cbutton2 = tk.Button(cframe, text="Find Y", command=handle_findy)
cbutton2.pack(side=tk.LEFT, fill='x', expand=True)
# Result area
scr=scrolledtext.ScrolledText(window, wrap=tk.WORD)
scr.config(state=tk.DISABLED)
scr.pack(fill='both', expand=True)
window.mainloop()