def __init__(self, jpath_or_analyser, testsuites, testsuite_paths):
self.win = ThemedTk(title='json explorer', esc_closes=True,
geometry=(-200, -200))
if sys.platform == 'win32':
self.win.wm_iconbitmap(bitmap = get_root_path('res', 'TPH_DNA.ico'))
self.win.columnconfigure(0, weight=1)
self.win.columnconfigure(1, weight=0)
self.win.rowconfigure(0, weight=0)
self.win.rowconfigure(1, weight=0)
self.win.rowconfigure(2, weight=4)
if isinstance(jpath_or_analyser, Analyser):
self.analyser = jpath_or_analyser
name = os.path.basename(self.analyser.fastq.fname)
else:
try:
data = json.load(file(jpath_or_analyser))
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
self.analyser = Analyser()
self.analyser.decode(testsuites, data)
self.analyser.update_testsuites()
except Exception, e:
exc_info = sys.exc_info()
self.win.destroy()
raise exc_info[1], None, exc_info[2]
name = os.path.basename(jpath_or_analyser)
from kvarq.genes import load_testsuite
from kvarq.analyse import Analyser
# rows : genomes
# columns : SNPs
#
# table1 : mean coverage
# table2 : sd/mean
# table3 : [AX][M]
# - D if derived has majority
# - X if non-ancestral-non-derived has majority
# - M if most prevalent < 90%
import json, csv, sys, os.path
analyser = Analyser()
coll_path = os.path.join(os.path.dirname(__file__), 'coll14.py')
name, testsuite = load_testsuite(coll_path)
tests = testsuite.tests
testsuites = {name: testsuite}
columns = ['filename']
columns += [str(test) for test in tests]
means = {}
sds = {}
types = {}
for fname in sys.argv[1:]:
class JsonExplorer:
# whishlist
# - file info
# - version, size, scantime
# - readlengths_hist=f(Amin), fastq_type
# - lineage
# - scores
# - resistances
# - analyse : (non) synonymous
def __init__(self, jpath_or_analyser, testsuites, testsuite_paths):
self.win = ThemedTk(title='json explorer', esc_closes=True,
geometry=(-200, -200))
if sys.platform == 'win32':
self.win.wm_iconbitmap(bitmap = get_root_path('res', 'TPH_DNA.ico'))
self.win.columnconfigure(0, weight=1)
self.win.columnconfigure(1, weight=0)
self.win.rowconfigure(0, weight=0)
self.win.rowconfigure(1, weight=0)
self.win.rowconfigure(2, weight=4)
if isinstance(jpath_or_analyser, Analyser):
self.analyser = jpath_or_analyser
name = os.path.basename(self.analyser.fastq.fname)
else:
try:
data = json.load(file(jpath_or_analyser))
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
self.analyser = Analyser()
self.analyser.decode(testsuites, data)
self.analyser.update_testsuites()
except Exception, e:
exc_info = sys.exc_info()
self.win.destroy()
raise exc_info[1], None, exc_info[2]
name = os.path.basename(jpath_or_analyser)
self.dlabel = tk.Label(self.win, text=name)
self.dlabel.grid(row=0, column=0, columnspan=2, sticky='ew')
self.menu = tk.Menu(self.win)
filemenu = tk.Menu(self.menu)
self.menu.add_cascade(label='KvarQ', menu=filemenu)
filemenu.add_command(label='Help', command=open_help)
self.win.config(menu=self.menu)
# list of analyses
self.yscroll1 = tk.Scrollbar(self.win, orient=tk.VERTICAL)
self.yscroll1.grid(row=1, column=1, sticky='ns')
self.alist = tk.Listbox(self.win, height=len(self.analyser.testsuites)+1, yscrollcommand=self.yscroll1.set)
self.alist.grid(row=1, column=0, sticky='nsew')
self.yscroll1["command"] = self.alist.yview
self.alist.bind("<Double-Button-1>", self.show_analyses)
self.alist.bind("<Return>", self.show_analyses)
# fill in list of analyses, prepare dict of coverages
self.anames = ['info']
self.alist.insert(tk.END, 'info')
for aname, testsuite in self.analyser.testsuites.items():
self.anames.append(aname)
result = self.analyser.results[aname]
if type(result)==list:
result = '; '.join(result)
self.alist.insert(tk.END, aname + ': ' + result)
# list of coverages
self.yscroll2 = tk.Scrollbar(self.win, orient=tk.VERTICAL)
self.yscroll2.grid(row=2, column=1, sticky='ns')
self.clist = tk.Listbox(self.win, yscrollcommand=self.yscroll2.set)
self.clist.grid(row=2, column=0, sticky='nsew')
self.yscroll2["command"] = self.clist.yview
self.clist.bind("<Double-Button-1>", self.show_coverage)
self.clist.bind("<Return>", self.show_coverage)
self.current = None
self.alist.activate(0)
self.alist.selection_set(0)
self.alist.focus_set()
self.after_id = None
def close_win(a=None):
if self.after_id:
self.win.after_cancel(self.after_id)
self.win.destroy()
self.win.close = close_win
self.win.protocol('WM_DELETE_WINDOW', close_win)
self.poll()
from kvarq.genes import load_testsuite
from kvarq.analyse import Analyser
# rows : genomes
# columns : SNPs
#
# table1 : mean coverage
# table2 : sd/mean
# table3 : [AX][M]
# - D if derived has majority
# - X if non-ancestral-non-derived has majority
# - M if most prevalent < 90%
import json, csv, sys, os.path
analyser = Analyser()
coll_path = os.path.join(os.path.dirname(__file__), 'coll14.py')
name, testsuite = load_testsuite(coll_path)
tests = testsuite.tests
testsuites = {name: testsuite}
columns = ['filename']
columns += [str(test) for test in tests]
means = {}
sds = {}
types = {}
for fname in sys.argv[1:]: