def main(argv):
wrapper = simplewrap.Wrapper()
wrap = wrapper.wrap
parser = argparse.ArgumentParser(description=wrap(DESCRIPTION),
formatter_class=argparse.RawTextHelpFormatter)
parser.set_defaults(**OPT_DEFAULTS)
wrapper.width = wrapper.width - 24
parser.add_argument('infile', metavar='read-families.tsv', nargs='?',
help=wrap('The output of align_families.py. 6 columns:\n'
'1. (canonical) barcode\n'
'2. order ("ab" or "ba")\n'
'3. mate ("1" or "2")\n'
'4. read name\n'
'5. aligned sequence\n'
'6. aligned quality scores.'))
parser.add_argument('-r', '--min-reads', type=int,
help=wrap('The minimum number of reads (from each strand) required to form a single-strand '
'consensus. Strands with fewer reads will be skipped. Default: %(default)s.'))
parser.add_argument('-q', '--qual', type=int,
help=wrap('Base quality threshold. Bases below this quality will not be counted. '
'Default: %(default)s.'))
parser.add_argument('-F', '--qual-format', choices=('sanger', 'solexa'),
help=wrap('FASTQ quality score format. Sanger scores are assumed to begin at \'{}\' ({}). '
'Default: %(default)s.'.format(SANGER_START, chr(SANGER_START))))
parser.add_argument('--incl-sscs', action='store_true',
help=wrap('When outputting duplex consensus sequences, include reads without a full duplex '
'(missing one strand). The result will just be the single-strand consensus of the '
'remaining read.'))
parser.add_argument('-s', '--sscs-file',
help=wrap('Save single-strand consensus sequences in this file (FASTA format). Currently does '
'not work when in parallel mode.'))
parser.add_argument('-l', '--log', metavar='LOG_FILE', dest='stats_file',
help=wrap('Print statistics on the run to this file. Use "-" to print to stderr.'))
parser.add_argument('-p', '--processes', type=int,
help=wrap('Number of processes to use. If > 1, launches this many worker subprocesses. Note: '
'if this option is used, no output will be generated until the end of the entire '
'run, so no streaming is possible. Default: %(default)s.'))
parser.add_argument('--phone-home', action='store_true',
help=wrap('Report helpful usage data to the developer, to better understand the use cases and '
'performance of the tool. The only data which will be recorded is the name and '
'version of the tool, the size of the input data, the time taken to process it, and '
'the IP address of the machine running it. No parameters or filenames are sent. All '
'the reporting and recording code is available at https://github.com/NickSto/ET.'))
parser.add_argument('--galaxy', dest='platform', action='store_const', const='galaxy',
help=wrap('Tell the script it\'s running on Galaxy. Currently this only affects data reported '
'when phoning home.'))
parser.add_argument('--test', action='store_true',
help=wrap('If reporting usage data, mark this as a test run.'))
parser.add_argument('-v', '--version', action='version', version=str(version.get_version()),
help=wrap('Print the version number and exit.'))
args = parser.parse_args(argv[1:])
start_time = time.time()
if args.phone_home:
run_id = phone.send_start(__file__, version.get_version(), platform=args.platform, test=args.test)
assert args.processes > 0, '-p must be greater than zero'
# Make dict of process_family() parameters that don't change between families.
static = {}
static['processes'] = args.processes
static['incl_sscs'] = args.incl_sscs
static['min_reads'] = args.min_reads
if args.sscs_file:
static['sscs_fh'] = open(args.sscs_file, 'w')
if args.qual_format == 'sanger':
static['qual_thres'] = chr(args.qual + SANGER_START)
elif args.qual_format == 'solexa':
static['qual_thres'] = chr(args.qual + SOLEXA_START)
else:
fail('Error: unrecognized --qual-format.')
if args.infile:
infile = open(args.infile)
else:
infile = sys.stdin
if args.stats_file:
if args.stats_file == '-':
logging.basicConfig(stream=sys.stderr, level=logging.INFO, format='%(message)s')
else:
logging.basicConfig(filename=args.stats_file, filemode='w', level=logging.INFO,
format='%(message)s')
else:
logging.disable(logging.CRITICAL)
# Open all the worker processes, if we're using more than one.
workers = None
if args.processes > 1:
workers = open_workers(args.processes, args)
stats = {'time':0, 'reads':0, 'runs':0, 'families':0}
all_reads = 0
duplex = collections.OrderedDict()
family = []
barcode = None
order = None
mate = None
for line in infile:
fields = line.rstrip('\r\n').split('\t')
if len(fields) != 6:
continue
(this_barcode, this_order, this_mate, name, seq, qual) = fields
this_mate = int(this_mate)
# If the barcode or order has changed, we're in a new single-stranded family.
# Process the reads we've previously gathered as one family and start a new family.
if this_barcode != barcode or this_order != order or this_mate != mate:
duplex[(order, mate)] = family
# We're at the end of the duplex pair if the barcode changes or if the order changes without
# the mate changing, or vice versa (the second read in each duplex comes when the barcode
# stays the same while both the order and mate switch). Process the duplex and start
# a new one. If the barcode is the same, we're in the same duplex, but we've switched strands.
if this_barcode != barcode or not (this_order != order and this_mate != mate):
# sys.stderr.write('New duplex: {}, {}, {}\n'.format(this_barcode, this_order, this_mate))
process_duplex(duplex, barcode, workers=workers, stats=stats, **static)
duplex = collections.OrderedDict()
# else:
# sys.stderr.write('Same duplex: {}, {}, {}\n'.format(this_barcode, this_order, this_mate))
barcode = this_barcode
order = this_order
mate = this_mate
family = []
read = {'name': name, 'seq':seq, 'qual':qual}
family.append(read)
all_reads += 1
# Process the last family.
duplex[(order, mate)] = family
process_duplex(duplex, barcode, workers=workers, stats=stats, **static)
if args.processes > 1:
close_workers(workers)
compile_results(workers)
delete_tempfiles(workers)
if args.sscs_file:
static['sscs_fh'].close()
if infile is not sys.stdin:
infile.close()
end_time = time.time()
run_time = int(end_time - start_time)
# Final stats on the run.
logging.info('Processed {} reads and {} duplexes in {} seconds.'
.format(all_reads, stats['runs'], run_time))
per_read = stats['time'] / stats['reads']
per_run = stats['time'] / stats['runs']
logging.info('{:0.3f}s per read, {:0.3f}s per run.'.format(per_read, per_run))
if args.phone_home:
stats['consensus_time'] = stats['time']
del stats['time']
phone.send_end(__file__, version.get_version(), run_id, run_time, stats, platform=args.platform,
test=args.test)
def build(self):
"""Build window."""
self.setWindowTitle("MSFS Mod Manager - {}".format(
get_version(self.appctxt)))
self.setWindowIcon(
QtGui.QIcon(
self.appctxt.get_resource(os.path.join("icons", "icon.png"))))
self.main_widget = main_widget(self, self.appctxt)
self.main_widget.build()
self.setCentralWidget(self.main_widget)
main_menu = self.menuBar()
file_menu = main_menu.addMenu("File")
self.theme_menu_action = QtWidgets.QAction("FS Theme",
self,
checkable=True)
self.theme_menu_action.setChecked(get_theme())
self.theme_menu_action.triggered.connect(self.set_theme)
file_menu.addAction(self.theme_menu_action)
file_menu.addSeparator()
menu_action = QtWidgets.QAction("Install Mod(s) from Archive", self)
menu_action.triggered.connect(self.main_widget.install_archive)
file_menu.addAction(menu_action)
menu_action = QtWidgets.QAction("Install Mod from Folder", self)
menu_action.triggered.connect(self.main_widget.install_folder)
file_menu.addAction(menu_action)
menu_action = QtWidgets.QAction("Uninstall Mods", self)
menu_action.triggered.connect(self.main_widget.uninstall)
file_menu.addAction(menu_action)
file_menu.addSeparator()
menu_action = QtWidgets.QAction("Create Backup", self)
menu_action.triggered.connect(self.main_widget.create_backup)
file_menu.addAction(menu_action)
file_menu.addSeparator()
menu_action = QtWidgets.QAction("Exit", self)
menu_action.triggered.connect(self.parent.quit)
file_menu.addAction(menu_action)
edit_menu = main_menu.addMenu("Edit")
menu_action = QtWidgets.QAction("Enable Selected Mods", self)
menu_action.triggered.connect(self.main_widget.enable)
edit_menu.addAction(menu_action)
menu_action = QtWidgets.QAction("Disable Selected Mods", self)
menu_action.triggered.connect(self.main_widget.disable)
edit_menu.addAction(menu_action)
info_menu = main_menu.addMenu("Info")
menu_action = QtWidgets.QAction("Refresh Mods", self)
menu_action.triggered.connect(self.main_widget.refresh)
info_menu.addAction(menu_action)
menu_action = QtWidgets.QAction("Mod Info", self)
menu_action.triggered.connect(self.main_widget.info)
info_menu.addAction(menu_action)
info_menu.addSeparator()
menu_action = QtWidgets.QAction("About", self)
menu_action.triggered.connect(self.main_widget.about)
info_menu.addAction(menu_action)
def get_versions(self):
self.app_version_field.setText(get_version(self.appctxt))
self.game_version_field.setText(self.flight_sim.get_game_version())
def build(self) -> None:
"""Build window."""
self.setWindowTitle("MSFS Mod Manager - {}".format(
get_version(self.appctxt))) # type: ignore
self.setWindowIcon(
QtGui.QIcon(
self.appctxt.get_resource(os.path.join("icons", "icon.png"))))
self.main_widget = main_widget(self, self.appctxt)
self.main_widget.build()
self.setCentralWidget(self.main_widget)
main_menu = self.menuBar()
file_menu = main_menu.addMenu("File")
self.theme_menu_action = QtWidgets.QAction(
"FS Theme", self, checkable=True) # type: ignore
self.theme_menu_action.setChecked(get_theme())
self.theme_menu_action.triggered.connect(
self.set_theme) # type: ignore
file_menu.addAction(self.theme_menu_action) # type: ignore
file_menu.addSeparator()
menu_action = QtWidgets.QAction("Install Mod(s) from Archive", self)
menu_action.triggered.connect(
self.main_widget.install_archive) # type: ignore
file_menu.addAction(menu_action) # type: ignore
menu_action = QtWidgets.QAction("Install Mod from Folder", self)
menu_action.triggered.connect(
self.main_widget.install_folder) # type: ignore
file_menu.addAction(menu_action) # type: ignore
menu_action = QtWidgets.QAction("Uninstall Mods", self)
menu_action.triggered.connect(
self.main_widget.uninstall) # type: ignore
file_menu.addAction(menu_action) # type: ignore
file_menu.addSeparator()
menu_action = QtWidgets.QAction("Create Backup", self)
menu_action.triggered.connect(
self.main_widget.create_backup) # type: ignore
file_menu.addAction(menu_action) # type: ignore
file_menu.addSeparator()
menu_action = QtWidgets.QAction("Exit", self)
menu_action.triggered.connect(self.parent.quit) # type: ignore
file_menu.addAction(menu_action) # type: ignore
edit_menu = main_menu.addMenu("Edit")
menu_action = QtWidgets.QAction("Enable Selected Mods", self)
menu_action.triggered.connect(self.main_widget.enable) # type: ignore
edit_menu.addAction(menu_action) # type: ignore
menu_action = QtWidgets.QAction("Disable Selected Mods", self)
menu_action.triggered.connect(self.main_widget.disable) # type: ignore
edit_menu.addAction(menu_action) # type: ignore
edit_menu.addSeparator()
menu_action = QtWidgets.QAction("Change Mod Install Folder", self)
menu_action.triggered.connect(
self.main_widget.select_mod_install) # type: ignore
edit_menu.addAction(menu_action) # type: ignore
info_menu = main_menu.addMenu("Info")
menu_action = QtWidgets.QAction("Refresh Mods", self)
menu_action.triggered.connect(self.main_widget.refresh) # type: ignore
info_menu.addAction(menu_action) # type: ignore
menu_action = QtWidgets.QAction("Mod Info", self)
menu_action.triggered.connect(self.main_widget.info) # type: ignore
info_menu.addAction(menu_action) # type: ignore
help_menu = main_menu.addMenu("Help")
menu_action = QtWidgets.QAction("About", self)
menu_action.triggered.connect(self.main_widget.about) # type: ignore
help_menu.addAction(menu_action) # type: ignore
menu_action = QtWidgets.QAction("Versions", self)
menu_action.triggered.connect(
self.main_widget.versions) # type: ignore
help_menu.addAction(menu_action) # type: ignore
help_menu.addSeparator()
menu_action = QtWidgets.QAction("Open Official Website", self)
menu_action.triggered.connect( # type: ignore
lambda: webbrowser.open(
"https://github.com/NathanVaughn/msfs-mod-manager/"))
help_menu.addAction(menu_action) # type: ignore
menu_action = QtWidgets.QAction("Open Issues/Suggestions", self)
menu_action.triggered.connect( # type: ignore
lambda: webbrowser.open(
"https://github.com/NathanVaughn/msfs-mod-manager/issues/"))
help_menu.addAction(menu_action) # type: ignore
help_menu.addSeparator()
menu_action = QtWidgets.QAction("Open Debug Log", self)
menu_action.triggered.connect(
lambda: os.startfile(DEBUG_LOG)) # type: ignore
help_menu.addAction(menu_action) # type: ignore
menu_action = QtWidgets.QAction("Open Config File", self)
menu_action.triggered.connect(
lambda: os.startfile(CONFIG_FILE)) # type: ignore
help_menu.addAction(menu_action) # type: ignore
help_menu.addSeparator()
menu_action = QtWidgets.QAction("Open Community Folder", self)
menu_action.triggered.connect( # type: ignore
lambda: os.startfile(self.main_widget.flight_sim.
get_sim_mod_folder()))
help_menu.addAction(menu_action) # type: ignore
menu_action = QtWidgets.QAction("Open Mod Install Folder", self)
menu_action.triggered.connect( # type: ignore
lambda: os.startfile(files.get_mod_install_folder()))
help_menu.addAction(menu_action) # type: ignore
def main(argv):
wrapper = simplewrap.Wrapper()
wrap = wrapper.wrap
parser = argparse.ArgumentParser(description=wrap(DESCRIPTION),
formatter_class=argparse.RawTextHelpFormatter)
parser.set_defaults(**OPT_DEFAULTS)
wrapper.width = wrapper.width - 24
parser.add_argument('infile', metavar='read-families.tsv', nargs='?',
help=wrap('The input reads, sorted into families. One line per read pair, 8 tab-delimited '
'columns:\n'
'1. canonical barcode\n'
'2. barcode order ("ab" for alpha+beta, "ba" for beta-alpha)\n'
'3. read 1 name\n'
'4. read 1 sequence\n'
'5. read 1 quality scores\n'
'6. read 2 name\n'
'7. read 2 sequence\n'
'8. read 2 quality scores'))
parser.add_argument('-p', '--processes', type=int,
help=wrap('Number of worker subprocesses to use. Must be at least 1. Default: %(default)s.'))
parser.add_argument('--phone-home', action='store_true',
help=wrap('Report helpful usage data to the developer, to better understand the use cases and '
'performance of the tool. The only data which will be recorded is the name and '
'version of the tool, the size of the input data, the time taken to process it, and '
'the IP address of the machine running it. No parameters or filenames are sent. All '
'the reporting and recording code is available at https://github.com/NickSto/ET.'))
parser.add_argument('--galaxy', dest='platform', action='store_const', const='galaxy',
help=wrap('Tell the script it\'s running on Galaxy. Currently this only affects data reported '
'when phoning home.'))
parser.add_argument('--test', action='store_true',
help=wrap('If reporting usage data, mark this as a test run.'))
parser.add_argument('-v', '--version', action='version', version=str(version.get_version()),
help=wrap('Print the version number and exit.'))
args = parser.parse_args(argv[1:])
start_time = time.time()
if args.phone_home:
run_id = phone.send_start(__file__, version.get_version(), platform=args.platform, test=args.test)
assert args.processes > 0, '-p must be greater than zero'
# Check for required commands.
missing_commands = []
for command in REQUIRED_COMMANDS:
if not distutils.spawn.find_executable(command):
missing_commands.append(command)
if missing_commands:
fail('Error: Missing commands: "'+'", "'.join(missing_commands)+'".')
if args.infile:
infile = open(args.infile)
else:
infile = sys.stdin
# Open all the worker processes.
workers = open_workers(args.processes)
# Main loop.
"""This processes whole duplexes (pairs of strands) at a time for a future option to align the
whole duplex at a time.
duplex data structure:
duplex = {
'ab': [
{'name1': 'read_name1a',
'seq1': 'GATT-ACA',
'qual1': 'sc!0 /J*',
'name2': 'read_name1b',
'seq2': 'ACTGACTA',
'qual2': '34I&SDF)'
},
{'name1': 'read_name2a',
...
}
]
}
e.g.:
seq = duplex[order][pair_num]['seq1']
"""
stats = {'duplexes':0, 'time':0, 'pairs':0, 'runs':0, 'aligned_pairs':0}
current_worker_i = 0
duplex = collections.OrderedDict()
family = []
barcode = None
order = None
for line in infile:
fields = line.rstrip('\r\n').split('\t')
if len(fields) != 8:
continue
(this_barcode, this_order, name1, seq1, qual1, name2, seq2, qual2) = fields
# If the barcode or order has changed, we're in a new family.
# Process the reads we've previously gathered as one family and start a new family.
if this_barcode != barcode or this_order != order:
duplex[order] = family
# If the barcode is different, we're at the end of the whole duplex. Process the it and start
# a new one. If the barcode is the same, we're in the same duplex, but we've switched strands.
if this_barcode != barcode:
# sys.stderr.write('processing {}: {} orders ({})\n'.format(barcode, len(duplex),
# '/'.join([str(len(duplex[order])) for order in duplex])))
output, run_stats, current_worker_i = delegate(workers, stats, duplex, barcode)
process_results(output, run_stats, stats)
duplex = collections.OrderedDict()
barcode = this_barcode
order = this_order
family = []
pair = {'name1': name1, 'seq1':seq1, 'qual1':qual1, 'name2':name2, 'seq2':seq2, 'qual2':qual2}
family.append(pair)
stats['pairs'] += 1
# Process the last family.
duplex[order] = family
# sys.stderr.write('processing {}: {} orders ({}) [last]\n'.format(barcode, len(duplex),
# '/'.join([str(len(duplex[order])) for order in duplex])))
output, run_stats, current_worker_i = delegate(workers, stats, duplex, barcode)
process_results(output, run_stats, stats)
# Do one last loop through the workers, reading the remaining results and stopping them.
# Start at the worker after the last one processed by the previous loop.
start = current_worker_i + 1
for i in range(len(workers)):
worker_i = (start + i) % args.processes
worker = workers[worker_i]
output, run_stats = worker['parent_pipe'].recv()
process_results(output, run_stats, stats)
worker['parent_pipe'].send(None)
if infile is not sys.stdin:
infile.close()
end_time = time.time()
run_time = int(end_time - start_time)
# Final stats on the run.
sys.stderr.write('Processed {pairs} read pairs in {duplexes} duplexes.\n'.format(**stats))
if stats['aligned_pairs'] > 0:
per_pair = stats['time'] / stats['aligned_pairs']
per_run = stats['time'] / stats['runs']
sys.stderr.write('{:0.3f}s per pair, {:0.3f}s per run.\n'.format(per_pair, per_run))
sys.stderr.write('{}s total time.\n'.format(run_time))
if args.phone_home:
stats['align_time'] = stats['time']
del stats['time']
phone.send_end(__file__, version.get_version(), run_id, run_time, stats, platform=args.platform,
test=args.test)
def main():
# Change umask to allow group read/write files
os.umask(0o007)
# Print welcome art and version
print(art.art)
print("Version: {}\n".format(version.get_version()).rjust(55))
# Remember sessions
session_name = input("Enter session name: ")
session = getSession(session_name)
if not session:
print("Enter one or more UNIX file name patterns\nto identify the scripts which need grading.\nSeparate patterns with a comma.")
patterns = str(input("> ")).replace(' ','').split(',')
print("Enter paths to all testing scripts you would\nlike to run against the homework,\nseparated by commas.")
tests = str(input("> "))
tests = tests.replace(' ','').split(',') if tests != '' else None
print("Enter the maximum point value for the assignment to verify that students are not given extra credit.")
maxpoints = input("> ")
maxpoints = float(maxpoints) if maxpoints != '' else -1
writeSession(session_name, patterns, tests, maxpoints)
else:
patterns = session['patterns']
tests = session['tests']
maxpoints = session['maxpoints']
# Allow for multiple grading sessions at once
if session_name:
grade_file_name = session_name + '_grade.csv'
else:
grade_file_name = 'grade.csv'
# Get the list of student files to grade
student_files = []
for pattern in patterns:
files = rfind.find(pattern,'.',IGNORE)
for f in files:
if f not in student_files:
student_files.append(f)
# Main menu
menu_main.print_menu()
opt = menu_main.get_option()
while opt != menu_main.options.TerminateProgram:
if opt == menu_main.options.GradeHomeworks:
gradeHomeworks(grade_file_name, student_files, tests, maxpoints)
menu_main.print_menu()
elif opt == menu_main.options.CheckGradeFiles:
checkGradeFiles(grade_file_name)
menu_main.print_menu()
elif opt == menu_main.options.GradingStatistics:
#printStatistics()
print("Not yet implemented")
elif opt == menu_main.options.ConsolidateGrades:
#consolidateGradeFiles()
print("Not yet implemented")
else:
print("You somehow got an impossible option:", opt)
opt = menu_main.get_option()
print("Grading session complete.")
def get_versions(self) -> None:
self.app_version_field.setText(get_version(
self.appctxt)) # type: ignore
self.game_version_field.setText(self.flight_sim.get_game_version())