def info(args):
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
if args.select_all:
testsuites = load_testsuites(testsuite_paths, testsuite_paths.keys())
else:
testsuites = load_testsuites(testsuite_paths, args.select or [])
print('version=' + VERSION)
testsuites_descr = []
tbp = tests = 0
for name, testsuite in testsuites.items():
bp = 0
for test in testsuite.tests:
if isinstance(test.template, genes.DynamicTemplate):
bp += len(test.template.seq(spacing=args.spacing))
else:
bp += len(test.template.seq())
testsuites_descr.append('%s-%s[%d:%dbp]' % (
name, testsuite.version, len(testsuite.tests), bp))
tbp += bp
tests += len(testsuite.tests)
print('testsuites=' + ','.join(testsuites_descr))
print('sum=%d tests,%dbp' % (tests, tbp))
print('sys.prefix=' + sys.prefix)
def illustrate(args):
data = json.load(file(args.file))
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
testsuites = {}
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
analyser = analyse.Analyser()
lo.info('loading json-file args.file')
analyser.decode(testsuites, data)
lo.info('updating testsuites')
analyser.update_testsuites()
if args.readlengths:
rls = analyser.stats['readlengths']
hist = TextHist()
print(hist.draw(rls, indexed=True))
if args.coverage:
for name, testsuite in analyser.testsuites.items():
print(name + ':')
for test in testsuite.tests:
print(' - %s : %s' % (test, analyser[test]))
print()
if args.results:
for testsuite, results in analyser.results.items():
print('\n'+testsuite)
print('-'*len(testsuite))
pprint(results)
def gui(args):
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
# only import Tkinter etc now
import Tkinter
from kvarq.gui.main import MainGUI
MainGUI(testsuite_paths=testsuite_paths)
Tkinter.mainloop()
def explorer(args):
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
import Tkinter as tk
from kvarq.gui.explorer import DirectoryExplorer, JsonExplorer
if os.path.isdir(args.explorable):
DirectoryExplorer(args.explorable,
testsuites={}, testsuite_paths=testsuite_paths)
else:
JsonExplorer(args.explorable,
testsuites={}, testsuite_paths=testsuite_paths)
tk.mainloop()
def scan(args):
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
if args.select_all:
testsuites = load_testsuites(testsuite_paths, testsuite_paths.keys())
else:
testsuites = load_testsuites(testsuite_paths, args.select)
if not testsuites:
sys.stderr.write('\n*** you must specify at least one testsuite! ***\n\n')
sys.stderr.write('(use the -t command line switch)\n\n')
sys.exit(ERROR_COMMAND_LINE_SWITCH)
# prepare scanning {{{2
try:
fastq = Fastq(args.fastq, paired=not args.no_paired, variant=args.variant)
except FastqFileFormatException, e:
lo.error('cannot open file %s : %s'%(args.fastq, str(e)))
sys.exit(ERROR_FASTQ_FORMAT_ERROR)
def update(args):
if args.fastq:
lo.warning('re-reading of hits not currently implemented')
data = json.load(file(args.json))
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
testsuites = {}
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
analyser = analyse.Analyser()
analyser.decode(testsuites, data)
analyser.update_testsuites()
# save results back to .json
data = analyser.encode(hits = analyser.hits is not None)
j = codecs.open(args.json, 'w', 'utf-8')
lo.info('re-wrote results to file ' + args.json)
json.dump(data, j, indent=2)
def do_showlog(self, e=None):
logwin = ThemedTk(title='contents of logfile (%s)' % logfn, geometry=(-200, -200))
frame = tk.Frame(logwin)
text = tk.Text(frame)
text.pack(side=tk.LEFT, fill=tk.BOTH, expand=True)
scroll = tk.Scrollbar(frame, command=text.yview)
scroll.pack(side=tk.RIGHT, fill=tk.Y)
text.config(yscrollcommand=scroll.set)
text.yscrollbar = scroll
frame.pack(side=tk.TOP, expand=True, fill=tk.BOTH)
for line in file(logfn).readlines():
text.insert(tk.END, line)
yy = text.yscrollbar.get()
text.yscrollbar.set(1-yy[1]+yy[0], 1)
text.yview('moveto', 1-yy[1]+yy[0])
def scrolldown(self):
# autoscrolldown
yy = self.text.yscrollbar.get()
self.text.yscrollbar.set(1-yy[1]+yy[0], 1)
self.text.yview('moveto', 1-yy[1]+yy[0])
if __name__=='__main__':
win = MainGUI(testsuite_paths=discover_testsuites())
tk.mainloop()
def setUpClass(cls):
lo.setLevel(logging.WARNING)
cls.testsuite_paths = discover_testsuites([testsuites_alt])
cls.testsuites = load_testsuites(cls.testsuite_paths, ['MTBC'])
