text_prompt stringlengths 157 13.1k | code_prompt stringlengths 7 19.8k ⌀ |
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def flatten_urlinfo(urlinfo, shorter_keys=True):
""" Takes a urlinfo object and returns a flat dictionary.""" |
def flatten(value, prefix=""):
if is_string(value):
_result[prefix[1:]] = value
return
try:
len(value)
except (AttributeError, TypeError): # a leaf
_result[prefix[1:]] = value
return
try:
items = value.items()... |
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def response_minify(self, response):
""" minify response html to decrease traffic """ |
if response.content_type == u'text/html; charset=utf-8':
endpoint = request.endpoint or ''
view_func = current_app.view_functions.get(endpoint, None)
name = (
'%s.%s' % (view_func.__module__, view_func.__name__)
if view_func else ''
... |
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def exempt(self, obj):
""" decorator to mark a view as exempt from htmlmin. """ |
name = '%s.%s' % (obj.__module__, obj.__name__)
@wraps(obj)
def __inner(*a, **k):
return obj(*a, **k)
self._exempt_routes.add(name)
return __inner |
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def dmql(query):
"""Client supplied raw DMQL, ensure quote wrap.""" |
if isinstance(query, dict):
raise ValueError("You supplied a dictionary to the dmql_query parameter, but a string is required."
" Did you mean to pass this to the search_filter parameter? ")
# automatically surround the given query with parentheses if it doe... |
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def ids(self, content_ids, object_ids):
"""Appends the content and object ids how RETS expects them""" |
result = []
content_ids = self.split(content_ids, False)
object_ids = self.split(object_ids)
for cid in content_ids:
result.append('{}:{}'.format(cid, ':'.join(object_ids)))
return result |
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def set_value(self, key, value):
""" Set key value to the file. The fuction will be make the key and value to dictinary formate. If its exist then it will update... |
file_cache = self.read_file()
if file_cache:
file_cache[key] = value
else:
file_cache = {}
file_cache[key] = value
self.update_file(file_cache) |
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def delete_value(self, key):
""" Delete the key if the token is expired. Arg: key : cache key """ |
response = {}
response['status'] = False
response['msg'] = "key does not exist"
file_cache = self.read_file()
if key in file_cache:
del file_cache[key]
self.update_file(file_cache)
response['status'] = True
response['msg'] = "succ... |
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def update_file(self, content):
""" It will convert json content to json string and update into file. Return: Boolean True/False """ |
updated_content = json.dumps(content)
file_obj = open(self.file, 'r+')
file_obj.write(str(updated_content))
file_obj.close()
return True |
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def auth(self):
""" Auth is used to call the AUTH API of CricketAPI. Access token required for every request call to CricketAPI. Auth functional will post user C... |
if not self.store_handler.has_value('access_token'):
params = {}
params["access_key"] = self.access_key
params["secret_key"] = self.secret_key
params["app_id"] = self.app_id
params["device_id"] = self.device_id
auth_url = self.api_path + "... |
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def get_active_token(self):
""" Getting the valid access token. Access token expires every 24 hours, It will expires then it will generate a new token. Return: a... |
expire_time = self.store_handler.has_value("expires")
access_token = self.store_handler.has_value("access_token")
if expire_time and access_token:
expire_time = self.store_handler.get_value("expires")
if not datetime.now() < datetime.fromtimestamp(float(expire_time)):
... |
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def get_recent_matches(self, card_type="micro_card"):
""" Calling the Recent Matches API. Arg: card_type: optional, default to micro_card. Accepted values are mi... |
recent_matches_url = self.api_path + "recent_matches/"
params = {}
params["card_type"] = card_type
response = self.get_response(recent_matches_url, params)
return response |
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def get_recent_season_matches(self, season_key):
""" Calling specific season recent matches. Arg: season_key: key of the season. Return: json date """ |
season_recent_matches_url = self.api_path + "season/" + season_key + "/recent_matches/"
response = self.get_response(season_recent_matches_url)
return response |
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def get_recent_seasons(self):
""" Calling the Recent Season API. Return: json data """ |
recent_seasons_url = self.api_path + "recent_seasons/"
response = self.get_response(recent_seasons_url)
return response |
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def get_schedule(self, date=None):
""" Calling the Schedule API. Return: json data """ |
schedule_url = self.api_path + "schedule/"
params = {}
if date:
params['date'] = date
response = self.get_response(schedule_url, params)
return response |
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def get_season_schedule(self, season_key):
""" Calling specific season schedule Arg: season_key: key of the season Return: json data """ |
schedule_url = self.api_path + "season/" + season_key + "/schedule/"
response = self.get_response(schedule_url)
return response |
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def get_season(self, season_key, card_type="micro_card"):
""" Calling Season API. Arg: season_key: key of the season card_type: optional, default to micro_card. ... |
season_url = self.api_path + "season/" + season_key + "/"
params = {}
params["card_type"] = card_type
response = self.get_response(season_url, params)
return response |
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def get_season_stats(self, season_key):
""" Calling Season Stats API. Arg: season_key: key of the season Return: json data """ |
season_stats_url = self.api_path + "season/" + season_key + "/stats/"
response = self.get_response(season_stats_url)
return response |
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def get_season_team(self, season_key, season_team_key,stats_type=None):
""" Calling Season teams API Arg: season_key: key of the season Return: json data """ |
params = {"stats_type": stats_type}
season_team_url = self.api_path + 'season/' + season_key + '/team/' + season_team_key + '/'
response = self.get_response(season_team_url, params=params)
return response |
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def get_season_points(self, season_key):
""" Calling Season Points API. Arg: season_key: key of the season Return: json data """ |
season_points_url = self.api_path + "season/" + season_key + "/points/"
response = self.get_response(season_points_url)
return response |
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def get_season_player_stats(self, season_key, player_key):
""" Calling Season Player Stats API. Arg: season_key: key of the season player_key: key of the player ... |
season_player_stats_url = self.api_path + "season/" + season_key + "/player/" + player_key + "/stats/"
response = self.get_response(season_player_stats_url)
return response |
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def get_overs_summary(self, match_key):
""" Calling Overs Summary API Arg: match_key: key of the match Return: json data """ |
overs_summary_url = self.api_path + "match/" + match_key + "/overs_summary/"
response = self.get_response(overs_summary_url)
return response |
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def get_news_aggregation(self):
""" Calling News Aggregation API Return: json data """ |
news_aggregation_url = self.api_path + "news_aggregation" + "/"
response = self.get_response(news_aggregation_url)
return response |
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def get_fantasy_credits(self, match_key):
""" Calling Fantasy Credit API Arg: match_key: key of the match Return: json data """ |
fantasy_credit_url = self.api_path_v3 + "fantasy-match-credits/" + match_key + "/"
response = self.get_response(fantasy_credit_url)
return response |
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def get_fantasy_points(self, match_key):
""" Calling Fantasy Points API Arg: match_key: key of the match Return: json data """ |
fantasy_points_url = self.api_path_v3 + "fantasy-match-points/" + match_key + "/"
response = self.get_response(fantasy_points_url)
return response |
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def main(self):
""" Generates an output string by replacing the keywords in the format string with the corresponding values from a submission dictionary. """ |
self.manage_submissions()
out_string = self.options['format']
# Pop until we get something which len(title) <= max-chars
length = float('inf')
while length > self.options['max_chars']:
self.selected_submission = self.submissions.pop()
length = len(self.s... |
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def login(self):
""" Logs into Reddit in order to display a personalised front page. """ |
data = {'user': self.options['username'], 'passwd':
self.options['password'], 'api_type': 'json'}
response = self.client.post('http://www.reddit.com/api/login', data=data)
self.client.modhash = response.json()['json']['data']['modhash'] |
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def manage_submissions(self):
""" If there are no or only one submissions left, get new submissions. This function manages URL creation and the specifics for fro... |
if not hasattr(self, 'submissions') or len(self.submissions) == 1:
self.submissions = []
if self.options['mode'] == 'front':
# If there are no login details, the standard front
# page will be displayed.
if self.options['password'] and self... |
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def get_submissions(self, url):
""" Connects to Reddit and gets a JSON representation of submissions. This JSON data is then processed and returned. url: A url t... |
response = self.client.get(url, params={'limit': self.options['limit']})
submissions = [x['data'] for x in response.json()['data']['children']]
return submissions |
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def main(self):
""" A compulsary function that gets the output of the cmus-remote -Q command and converts it to unicode in order for it to be processed and final... |
try:
# Setting stderr to subprocess.STDOUT seems to stop the error
# message returned by the process from being output to STDOUT.
cmus_output = subprocess.check_output(['cmus-remote', '-Q'],
stderr=subprocess.STDOUT).decode('utf-8')
... |
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def convert_cmus_output(self, cmus_output):
""" Change the newline separated string of output data into a dictionary which can then be used to replace the string... |
cmus_output = cmus_output.split('\n')
cmus_output = [x.replace('tag ', '') for x in cmus_output if not x in '']
cmus_output = [x.replace('set ', '') for x in cmus_output]
status = {}
partitioned = (item.partition(' ') for item in cmus_output)
status = {item[0]: item[2] f... |
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def output(self, full_text, short_text):
""" Output all of the options and data for a segment. full_text: A string representing the data that should be output to... |
full_text = full_text.replace('\n', '')
short_text = short_text.replace('\n', '')
self.output_options.update({'full_text': full_text, 'short_text': short_text})
self.output_options = {k: v for k, v in self.output_options.items() if v}
return self.output_options |
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def on_click(self, event):
""" A function that should be overwritten by a plugin that wishes to react to events, if it wants to perform any action other than run... |
if event['button'] == 1 and 'button1' in self.options:
subprocess.call(self.options['button1'].split())
elif event['button'] == 2 and 'button2' in self.options:
subprocess.call(self.options['button2'].split())
elif event['button'] == 3 and 'button3' in self.options:
... |
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def url_image(request, image_id, thumb_options=None, width=None, height=None):
""" Converts a filer image ID in a complete path :param request: Request object :p... |
image = File.objects.get(pk=image_id)
if getattr(image, 'canonical_url', None):
url = image.canonical_url
else:
url = image.url
thumb = _return_thumbnail(image, thumb_options, width, height)
if thumb:
image = thumb
url = image.url
data = {
'url': url,
... |
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def thumbnail_options(request):
""" Returns the requested ThumbnailOption as JSON :param request: Request object :return: JSON serialized ThumbnailOption """ |
response_data = [{'id': opt.pk, 'name': opt.name} for opt in ThumbnailOption.objects.all()]
return http.HttpResponse(json.dumps(response_data), content_type="application/json") |
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def serve_image(request, image_id, thumb_options=None, width=None, height=None):
""" returns the content of an image sized according to the parameters :param req... |
image = File.objects.get(pk=image_id)
if getattr(image, 'canonical_url', None):
url = image.canonical_url
else:
url = image.url
thumb = _return_thumbnail(image, thumb_options, width, height)
if thumb:
return server.serve(request, file_obj=thumb, save_as=False)
else:
... |
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def _touch_dir(self, path):
""" A helper function to create a directory if it doesn't exist. path: A string containing a full path to the directory to be created... |
try:
os.makedirs(path)
except OSError as e:
if e.errno != errno.EEXIST:
raise |
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def reload(self):
""" Reload the configuration from the file. This is in its own function so that it can be called at any time by another class. """ |
self._conf = configparser.ConfigParser()
# Preserve the case of sections and keys.
self._conf.optionxform = str
self._conf.read(self.config_file_path)
if 'general' not in self._conf.keys():
raise IncompleteConfigurationFile('Missing the general section')
gene... |
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def coerce_retention_period(value):
""" Coerce a retention period to a Python value. :param value: A string containing the text 'always', a number or an expressi... |
# Numbers pass through untouched.
if not isinstance(value, numbers.Number):
# Other values are expected to be strings.
if not isinstance(value, string_types):
msg = "Expected string, got %s instead!"
raise ValueError(msg % type(value))
# Check for the literal str... |
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def load_config_file(configuration_file=None, expand=True):
""" Load a configuration file with backup directories and rotation schemes. :param configuration_file... |
expand_notice_given = False
if configuration_file:
loader = ConfigLoader(available_files=[configuration_file], strict=True)
else:
loader = ConfigLoader(program_name='rotate-backups', strict=False)
for section in loader.section_names:
items = dict(loader.get_options(section))
... |
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def rotate_concurrent(self, *locations, **kw):
""" Rotate the backups in the given locations concurrently. :param locations: One or more values accepted by :func... |
timer = Timer()
pool = CommandPool(concurrency=10)
logger.info("Scanning %s ..", pluralize(len(locations), "backup location"))
for location in locations:
for cmd in self.rotate_backups(location, prepare=True, **kw):
pool.add(cmd)
if pool.num_commands ... |
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def load_config_file(self, location):
""" Load a rotation scheme and other options from a configuration file. :param location: Any value accepted by :func:`coerc... |
location = coerce_location(location)
for configured_location, rotation_scheme, options in load_config_file(self.config_file, expand=False):
if configured_location.match(location):
logger.verbose("Loading configuration for %s ..", location)
if rotation_scheme:... |
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def collect_backups(self, location):
""" Collect the backups at the given location. :param location: Any value accepted by :func:`coerce_location()`. :returns: A... |
backups = []
location = coerce_location(location)
logger.info("Scanning %s for backups ..", location)
location.ensure_readable()
for entry in natsort(location.context.list_entries(location.directory)):
match = TIMESTAMP_PATTERN.search(entry)
if match:
... |
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def find_preservation_criteria(self, backups_by_frequency):
""" Collect the criteria used to decide which backups to preserve. :param backups_by_frequency: A :cl... |
backups_to_preserve = collections.defaultdict(list)
for frequency, delta in ORDERED_FREQUENCIES:
for period in backups_by_frequency[frequency].values():
for backup in period:
backups_to_preserve[backup].append(frequency)
return backups_to_preserve |
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def match(self, location):
""" Check if the given location "matches". :param location: The :class:`Location` object to try to match. :returns: :data:`True` if th... |
if self.ssh_alias != location.ssh_alias:
# Never match locations on other systems.
return False
elif self.have_wildcards:
# Match filename patterns using fnmatch().
return fnmatch.fnmatch(location.directory, self.directory)
else:
# Com... |
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def setup_file_logger(filename, formatting, log_level):
""" A helper function for creating a file logger. Accepts arguments, as it is used in Status and LoggingW... |
logger = logging.getLogger()
# If a stream handler has been attached, remove it.
if logger.handlers:
logger.removeHandler(logger.handlers[0])
handler = logging.FileHandler(filename)
logger.addHandler(handler)
formatter = logging.Formatter(*formatting)
handler.setFormatter(formatter)... |
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def output_to_bar(self, message, comma=True):
""" Outputs data to stdout, without buffering. message: A string containing the data to be output. comma: Whether o... |
if comma:
message += ','
sys.stdout.write(message + '\n')
sys.stdout.flush() |
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def reload(self):
""" Reload the installed plugins and the configuration file. This is called when either the plugins or config get updated. """ |
logging.debug('Reloading config file as files have been modified.')
self.config.plugin, self.config.general = self.config.reload()
logging.debug('Reloading plugins as files have been modified.')
self.loader = plugin_manager.PluginLoader(
self._plugin_path, self.config.plugin... |
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def run_plugins(self):
""" Creates a thread for each plugin and lets the thread_manager handle it. """ |
for obj in self.loader.objects:
# Reserve a slot in the output_dict in order to ensure that the
# items are in the correct order.
self.output_dict[obj.output_options['name']] = None
self.thread_manager.add_thread(obj.main, obj.options['interval']) |
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def run(self):
""" Monitors if the config file or plugins are updated. Also outputs the JSON data generated by the plugins, without needing to poll the threads. ... |
self.run_plugins()
while True:
# Reload plugins and config if either the config file or plugin
# directory are modified.
if self._config_mod_time != os.path.getmtime(self._config_file_path) or \
self._plugin_mod_time != os.path.getmtime(self._plug... |
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def _remove_empty_output(self):
""" If plugins haven't been initialised and therefore not sending output or their output is None, there is no reason to take up e... |
output = []
for key in self.output_dict:
if self.output_dict[key] is not None and 'full_text' in self.output_dict[key]:
output.append(self.output_dict[key])
return output |
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Description:
def handle_events(self):
""" An event handler that processes events from stdin and calls the on_click function of the respective object. This function is run in ... |
for event in sys.stdin:
if event.startswith('['):
continue
name = json.loads(event.lstrip(','))['name']
for obj in self.loader.objects:
if obj.output_options['name'] == name:
obj.on_click(json.loads(event.lstrip(','))) |
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def field_dict(self, model):
""" Helper function that returns a dictionary of all fields in the given model. If self.field_filter is set, it only includes the fi... |
if self.field_filter:
return dict(
[(f.name, f) for f in model._meta.fields
if self.field_filter(f)]
)
else:
return dict(
[(f.name, f) for f in model._meta.fields
if not f.rel and
n... |
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def run(self):
""" Calls the main function of a plugin and mutates the output dict with its return value. Provides an easy way to change the output whilst not ne... |
self.running = True
while self.running:
ret = self.func()
self.output_dict[ret['name']] = ret
time.sleep(self.interval)
return |
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def add_thread(self, func, interval):
""" Creates a thread, starts it and then adds it to the thread pool. Func: Same as in the Thread class. Interval: Same as i... |
t = Thread(func, interval, self.output_dict)
t.start()
self._thread_pool.append(t) |
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def _compile_files(self):
""" Compiles python plugin files in order to be processed by the loader. It compiles the plugins if they have been updated or haven't y... |
for f in glob.glob(os.path.join(self.dir_path, '*.py')):
# Check for compiled Python files that aren't in the __pycache__.
if not os.path.isfile(os.path.join(self.dir_path, f + 'c')):
compileall.compile_dir(self.dir_path, quiet=True)
logging.debug('Compil... |
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def _load_compiled(self, file_path):
""" Accepts a path to a compiled plugin and returns a module object. file_path: A string that represents a complete file pat... |
name = os.path.splitext(os.path.split(file_path)[-1])[0]
plugin_directory = os.sep.join(os.path.split(file_path)[0:-1])
compiled_directory = os.path.join(plugin_directory, '__pycache__')
# Use glob to autocomplete the filename.
compiled_file = glob.glob(os.path.join(compiled_dir... |
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def load_objects(self):
""" Matches the plugins that have been specified in the config file with the available plugins. Returns instantiated objects based upon t... |
objects = []
for settings in self._config:
if settings['plugin'] in self.plugins:
module = self.plugins[settings['plugin']]
# Trusts that the only item in __all__ is the name of the
# plugin class.
plugin_class = getattr(module... |
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def refresh_files(self):
""" Discovers the available plugins and turns each into a module object. This is a seperate function to allow plugins to be updated dyna... |
plugins = {}
_plugin_files = glob.glob(os.path.join(self.dir_path, '[!_]*.pyc'))
for f in glob.glob(os.path.join(self.dir_path, '[!_]*.py')):
if not any(os.path.splitext(f)[0] == os.path.splitext(x)[0]
for x in _plugin_files):
logging.debug('Addin... |
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def model_page(self, request, app_label, model_name, rest_of_url=None):
""" Handles the model-specific functionality of the databrowse site, delegating<to the ap... |
try:
model = get_model(app_label, model_name)
except LookupError:
model = None
if model is None:
raise http.Http404("App %r, model %r, not found." %
(app_label, model_name))
try:
databrowse_class = self.regi... |
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def values(self):
""" Returns a list of values for this field for this instance. It's a list so we can accomodate many-to-many fields. """ |
# This import is deliberately inside the function because it causes
# some settings to be imported, and we don't want to do that at the
# module level.
if self.field.rel:
if isinstance(self.field.rel, models.ManyToOneRel):
objs = getattr(self.instance.instanc... |
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def field_dict(self, model):
""" Helper function that returns a dictionary of all DateFields or DateTimeFields in the given model. If self.field_names is set, it... |
if self.field_names is None:
return dict([(f.name, f) for f in model._meta.fields
if isinstance(f, models.DateField)])
else:
return dict([(f.name, f)
for f in model._meta.fields
if isinstance(f, models.Da... |
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| def kmer_dag(job,
input_file,
output_path,
kmer_length,
spark_conf,
workers,
cores,
memory,
sudo):
'''
Optionally launches a Spark cluster and then runs ADAM to count k-mers on an
input file.
:param ... |
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| def download_count_upload(job,
master_ip,
input_file,
output_file,
kmer_length,
spark_conf,
memory,
sudo):
'''
Runs k-mer counting... |
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def run_gatk_germline_pipeline(job, samples, config):
""" Downloads shared files and calls the GATK best practices germline pipeline for a cohort of samples :par... |
# Determine the available disk space on a worker node before any jobs have been run.
work_dir = job.fileStore.getLocalTempDir()
st = os.statvfs(work_dir)
config.available_disk = st.f_bavail * st.f_frsize
# Check that there is a reasonable number of samples for joint genotyping
num_samples = le... |
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def gatk_germline_pipeline(job, samples, config):
""" Runs the GATK best practices pipeline for germline SNP and INDEL discovery. Steps in Pipeline 0: Generate a... |
require(len(samples) > 0, 'No samples were provided!')
# Get total size of genome reference files. This is used for configuring disk size.
genome_ref_size = config.genome_fasta.size + config.genome_fai.size + config.genome_dict.size
# 0: Generate processed BAM and BAI files for each sample
# grou... |
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def joint_genotype_and_filter(job, gvcfs, config):
""" Checks for enough disk space for joint genotyping, then calls the genotype and filter pipeline function. :... |
# Get the total size of genome reference files
genome_ref_size = config.genome_fasta.size + config.genome_fai.size + config.genome_dict.size
# Require at least 2.5x the sum of the individual GVCF files
cohort_size = sum(gvcf.size for gvcf in gvcfs.values())
require(int(2.5 * cohort_size + genome_r... |
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def genotype_and_filter(job, gvcfs, config):
""" Genotypes one or more GVCF files and runs either the VQSR or hard filtering pipeline. Uploads the genotyped VCF ... |
# Get the total size of the genome reference
genome_ref_size = config.genome_fasta.size + config.genome_fai.size + config.genome_dict.size
# GenotypeGVCF disk requirement depends on the input GVCF, the genome reference files, and
# the output VCF file. The output VCF is smaller than the input GVCF.
... |
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def annotate_vcfs(job, vcfs, config):
""" Runs Oncotator for a group of VCF files. Each sample is annotated individually. :param JobFunctionWrappingJob job: pass... |
job.fileStore.logToMaster('Running Oncotator on the following samples:\n%s' % '\n'.join(vcfs.keys()))
for uuid, vcf_id in vcfs.iteritems():
# The Oncotator disk requirement depends on the input VCF, the Oncotator database
# and the output VCF. The annotated VCF will be significantly larger than... |
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def parse_manifest(path_to_manifest):
""" Parses manifest file for Toil Germline Pipeline :param str path_to_manifest: Path to sample manifest file :return: List... |
bam_re = r"^(?P<uuid>\S+)\s(?P<url>\S+[bsc][r]?am)"
fq_re = r"^(?P<uuid>\S+)\s(?P<url>\S+)\s(?P<paired_url>\S+)?\s?(?P<rg_line>@RG\S+)"
samples = []
with open(path_to_manifest, 'r') as f:
for line in f.readlines():
line = line.strip()
if line.startswith('#'):
... |
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def download_shared_files(job, config):
""" Downloads shared reference files for Toil Germline pipeline :param JobFunctionWrappingJob job: passed automatically b... |
job.fileStore.logToMaster('Downloading shared reference files')
shared_files = {'genome_fasta', 'genome_fai', 'genome_dict'}
nonessential_files = {'genome_fai', 'genome_dict'}
# Download necessary files for pipeline configuration
if config.run_bwa:
shared_files |= {'amb', 'ann', 'bwt', 'pa... |
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def reference_preprocessing(job, config):
""" Creates a genome fasta index and sequence dictionary file if not already present in the pipeline config. :param Job... |
job.fileStore.logToMaster('Preparing Reference Files')
genome_id = config.genome_fasta
if getattr(config, 'genome_fai', None) is None:
config.genome_fai = job.addChildJobFn(run_samtools_faidx,
genome_id,
cor... |
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def prepare_bam(job, uuid, url, config, paired_url=None, rg_line=None):
""" Prepares BAM file for Toil germline pipeline. Steps in pipeline 0: Download and align... |
# 0: Align FASTQ or realign BAM
if config.run_bwa:
get_bam = job.wrapJobFn(setup_and_run_bwakit,
uuid,
url,
rg_line,
config,
paired_url=paired_... |
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def setup_and_run_bwakit(job, uuid, url, rg_line, config, paired_url=None):
""" Downloads and runs bwakit for BAM or FASTQ files :param JobFunctionWrappingJob jo... |
bwa_config = deepcopy(config)
bwa_config.uuid = uuid
bwa_config.rg_line = rg_line
# bwa_alignment uses a different naming convention
bwa_config.ref = config.genome_fasta
bwa_config.fai = config.genome_fai
# Determine if sample is a FASTQ or BAM file using the file extension
basename, ... |
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def gatk_haplotype_caller(job, bam, bai, ref, fai, ref_dict, annotations=None, emit_threshold=10.0, call_threshold=30.0, unsafe_mode=False, hc_output=None):
""" ... |
job.fileStore.logToMaster('Running GATK HaplotypeCaller')
inputs = {'genome.fa': ref,
'genome.fa.fai': fai,
'genome.dict': ref_dict,
'input.bam': bam,
'input.bam.bai': bai}
work_dir = job.fileStore.getLocalTempDir()
for name, file_store_id in in... |
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def static_dag(job, uuid, rg_line, inputs):
""" Prefer this here as it allows us to pull the job functions from other jobs without rewrapping the job functions b... |
# get work directory
work_dir = job.fileStore.getLocalTempDir()
inputs.cpu_count = cpu_count()
inputs.maxCores = sys.maxint
args = {'uuid': uuid,
's3_bucket': inputs.s3_bucket,
'sequence_dir': inputs.sequence_dir,
'dir_suffix': inputs.dir_suffix}
# get hea... |
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def download_encrypted_file(work_dir, url, key_path, name):
""" Downloads encrypted file from S3 Input1: Working directory Input2: S3 URL to be downloaded Input3... |
file_path = os.path.join(work_dir, name)
key = generate_unique_key(key_path, url)
encoded_key = base64.b64encode(key)
encoded_key_md5 = base64.b64encode(hashlib.md5(key).digest())
h1 = 'x-amz-server-side-encryption-customer-algorithm:AES256'
h2 = 'x-amz-server-side-encryption-customer-key:{}'.f... |
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def return_input_paths(job, work_dir, ids, *args):
""" Returns the paths of files from the FileStore Input1: Toil job instance Input2: Working directory Input3: ... |
paths = OrderedDict()
for name in args:
if not os.path.exists(os.path.join(work_dir, name)):
file_path = job.fileStore.readGlobalFile(ids[name], os.path.join(work_dir, name))
else:
file_path = os.path.join(work_dir, name)
paths[name] = file_path
if len(ar... |
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def move_to_output_dir(work_dir, output_dir, uuid=None, files=list()):
""" Moves files from work_dir to output_dir Input1: Working directory Input2: Output direc... |
for fname in files:
if uuid is None:
shutil.move(os.path.join(work_dir, fname), os.path.join(output_dir, fname))
else:
shutil.move(os.path.join(work_dir, fname), os.path.join(output_dir, '{}.{}'.format(uuid, fname))) |
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def batch_start(job, input_args):
""" Downloads shared files that are used by all samples for alignment and places them in the jobstore. """ |
shared_files = ['ref.fa', 'ref.fa.amb', 'ref.fa.ann', 'ref.fa.bwt', 'ref.fa.pac', 'ref.fa.sa', 'ref.fa.fai']
shared_ids = {}
for fname in shared_files:
url = input_args[fname]
shared_ids[fname] = job.addChildJobFn(download_from_url, url, fname).rv()
job.addFollowOnJobFn(spawn_batch_jobs... |
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def spawn_batch_jobs(job, shared_ids, input_args):
""" Spawns an alignment job for every sample in the input configuration file """ |
samples = []
config = input_args['config']
with open(config, 'r') as f_in:
for line in f_in:
line = line.strip().split(',')
uuid = line[0]
urls = line[1:]
samples.append((uuid, urls))
for sample in samples:
job.addChildJobFn(alignment, sha... |
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def alignment(job, ids, input_args, sample):
""" Runs BWA and then Bamsort on the supplied fastqs for this sample Input1: Toil Job instance Input2: jobstore id d... |
uuid, urls = sample
# ids['bam'] = job.fileStore.getEmptyFileStoreID()
work_dir = job.fileStore.getLocalTempDir()
output_dir = input_args['output_dir']
key_path = input_args['ssec']
cores = multiprocessing.cpu_count()
# I/O
return_input_paths(job, work_dir, ids, 'ref.fa', 'ref.fa.amb',... |
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def upload_bam_to_s3(job, ids, input_args, sample):
""" Uploads output BAM from sample to S3 Input1: Toil Job instance Input2: jobstore id dictionary Input3: Inp... |
uuid, urls = sample
key_path = input_args['ssec']
work_dir = job.fileStore.getLocalTempDir()
# Parse s3_dir to get bucket and s3 path
s3_dir = input_args['s3_dir']
bucket_name = s3_dir.lstrip('/').split('/')[0]
bucket_dir = '/'.join(s3_dir.lstrip('/').split('/')[1:])
base_url = 'https:/... |
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def tarball_files(work_dir, tar_name, uuid=None, files=None):
""" Tars a group of files together into a tarball work_dir: str Current Working Directory tar_name:... |
with tarfile.open(os.path.join(work_dir, tar_name), 'w:gz') as f_out:
for fname in files:
if uuid:
f_out.add(os.path.join(work_dir, fname), arcname=uuid + '.' + fname)
else:
f_out.add(os.path.join(work_dir, fname), arcname=fname) |
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def start_batch(job, input_args):
""" This function will administer 5 jobs at a time then recursively call itself until subset is empty """ |
samples = parse_sra(input_args['sra'])
# for analysis_id in samples:
job.addChildJobFn(download_and_transfer_sample, input_args, samples, cores=1, disk='30') |
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def download_and_transfer_sample(job, input_args, samples):
""" Downloads a sample from dbGaP via SRAToolKit, then uses S3AM to transfer it to S3 input_args: dic... |
if len(samples) > 1:
a = samples[len(samples)/2:]
b = samples[:len(samples)/2]
job.addChildJobFn(download_and_transfer_sample, input_args, a, disk='30G')
job.addChildJobFn(download_and_transfer_sample, input_args, b, disk='30G')
else:
analysis_id = samples[0]
wor... |
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def output_file_job(job, filename, file_id, output_dir, s3_key_path=None):
""" Uploads a file from the FileStore to an output directory on the local filesystem o... |
job.fileStore.logToMaster('Writing {} to {}'.format(filename, output_dir))
work_dir = job.fileStore.getLocalTempDir()
filepath = job.fileStore.readGlobalFile(file_id, os.path.join(work_dir, filename))
if urlparse(output_dir).scheme == 's3':
s3am_upload(job=job, fpath=os.path.join(work_dir, file... |
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def download_encrypted_file(job, input_args, name):
""" Downloads encrypted files from S3 via header injection input_args: dict Input dictionary defined in main(... |
work_dir = job.fileStore.getLocalTempDir()
key_path = input_args['ssec']
file_path = os.path.join(work_dir, name)
url = input_args[name]
with open(key_path, 'r') as f:
key = f.read()
if len(key) != 32:
raise RuntimeError('Invalid Key! Must be 32 bytes: {}'.format(key))
key... |
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def download_from_url(job, url):
""" Simple curl request made for a given url url: str URL to download """ |
work_dir = job.fileStore.getLocalTempDir()
file_path = os.path.join(work_dir, os.path.basename(url))
if not os.path.exists(file_path):
if url.startswith('s3:'):
download_from_s3_url(file_path, url)
else:
try:
subprocess.check_call(['curl', '-fs', '--r... |
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def docker_call(work_dir, tool_parameters, tool, java_opts=None, outfile=None, sudo=False):
""" Makes subprocess call of a command to a docker container. tool_pa... |
base_docker_call = 'docker run --log-driver=none --rm -v {}:/data'.format(work_dir).split()
if sudo:
base_docker_call = ['sudo'] + base_docker_call
if java_opts:
base_docker_call = base_docker_call + ['-e', 'JAVA_OPTS={}'.format(java_opts)]
try:
if outfile:
subproces... |
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def copy_to_output_dir(work_dir, output_dir, uuid=None, files=list()):
""" A list of files to move from work_dir to output_dir. work_dir: str Current working dir... |
for fname in files:
if uuid is None:
shutil.copy(os.path.join(work_dir, fname), os.path.join(output_dir, fname))
else:
shutil.copy(os.path.join(work_dir, fname), os.path.join(output_dir, '{}.{}'.format(uuid, fname))) |
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def program_checks(job, input_args):
""" Checks that dependency programs are installed. input_args: dict Dictionary of input arguments (from main()) """ |
# Program checks
for program in ['curl', 'docker', 'unzip', 'samtools']:
assert which(program), 'Program "{}" must be installed on every node.'.format(program)
job.addChildJobFn(download_shared_files, input_args) |
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def download_shared_files(job, input_args):
""" Downloads and stores shared inputs files in the FileStore input_args: dict Dictionary of input arguments (from ma... |
shared_files = ['unc.bed', 'hg19.transcripts.fa', 'composite_exons.bed', 'normalize.pl', 'rsem_ref.zip',
'ebwt.zip', 'chromosomes.zip']
shared_ids = {}
for f in shared_files:
shared_ids[f] = job.addChildJobFn(download_from_url, input_args[f]).rv()
if input_args['config'] or ... |
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def parse_config_file(job, ids, input_args):
""" Launches pipeline for each sample. shared_ids: dict Dictionary of fileStore IDs input_args: dict Dictionary of i... |
samples = []
config = input_args['config']
with open(config, 'r') as f:
for line in f.readlines():
if not line.isspace():
sample = line.strip().split(',')
samples.append(sample)
for sample in samples:
job.addChildJobFn(download_sample, ids, in... |
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def download_sample(job, ids, input_args, sample):
""" Defines variables unique to a sample that are used in the rest of the pipelines ids: dict Dictionary of fi... |
if len(sample) == 2:
uuid, sample_location = sample
url1, url2 = None, None
else:
uuid, url1, url2 = sample
sample_location = None
# Update values unique to sample
sample_input = dict(input_args)
sample_input['uuid'] = uuid
sample_input['sample.tar'] = sample_loc... |
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def static_dag_launchpoint(job, job_vars):
""" Statically define jobs in the pipeline job_vars: tuple Tuple of dictionaries: input_args and ids """ |
input_args, ids = job_vars
if input_args['config_fastq']:
cores = input_args['cpu_count']
a = job.wrapJobFn(mapsplice, job_vars, cores=cores, disk='130G').encapsulate()
else:
a = job.wrapJobFn(merge_fastqs, job_vars, disk='70 G').encapsulate()
b = job.wrapJobFn(consolidate_outpu... |
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def merge_fastqs(job, job_vars):
""" Unzips input sample and concats the Read1 and Read2 groups together. job_vars: tuple Tuple of dictionaries: input_args and i... |
input_args, ids = job_vars
work_dir = job.fileStore.getLocalTempDir()
cores = input_args['cpu_count']
single_end_reads = input_args['single_end_reads']
# I/O
sample = return_input_paths(job, work_dir, ids, 'sample.tar')
# Untar File
# subprocess.check_call(['unzip', sample, '-d', work_d... |
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def mapsplice(job, job_vars):
""" Maps RNA-Seq reads to a reference genome. job_vars: tuple Tuple of dictionaries: input_args and ids """ |
# Unpack variables
input_args, ids = job_vars
work_dir = job.fileStore.getLocalTempDir()
cores = input_args['cpu_count']
sudo = input_args['sudo']
single_end_reads = input_args['single_end_reads']
files_to_delete = ['R1.fastq']
# I/O
return_input_paths(job, work_dir, ids, 'ebwt.zip'... |
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def add_read_groups(job, job_vars):
""" This function adds read groups to the headers job_vars: tuple Tuple of dictionaries: input_args and ids """ |
input_args, ids = job_vars
work_dir = job.fileStore.getLocalTempDir()
sudo = input_args['sudo']
# I/O
alignments = return_input_paths(job, work_dir, ids, 'alignments.bam')
output = os.path.join(work_dir, 'rg_alignments.bam')
# Command and callg
parameter = ['AddOrReplaceReadGroups',
... |
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def bamsort_and_index(job, job_vars):
""" Sorts bam file and produces index file job_vars: tuple Tuple of dictionaries: input_args and ids """ |
# Unpack variables
input_args, ids = job_vars
work_dir = job.fileStore.getLocalTempDir()
sudo = input_args['sudo']
# I/O
rg_alignments = return_input_paths(job, work_dir, ids, 'rg_alignments.bam')
output = os.path.join(work_dir, 'sorted.bam')
# Command -- second argument is "Output Pref... |
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def sort_bam_by_reference(job, job_vars):
""" Sorts the bam by reference job_vars: tuple Tuple of dictionaries: input_args and ids """ |
# Unpack variables
input_args, ids = job_vars
work_dir = job.fileStore.getLocalTempDir()
# I/O
sorted_bam, sorted_bai = return_input_paths(job, work_dir, ids, 'sorted.bam', 'sorted.bam.bai')
output = os.path.join(work_dir, 'sort_by_ref.bam')
# Call: Samtools
ref_seqs = []
handle = s... |
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