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jeffrimko/Qprompt | lib/qprompt.py | ask_yesno | def ask_yesno(msg="Proceed?", dft=None):
"""Prompts the user for a yes or no answer. Returns True for yes, False
for no."""
yes = ["y", "yes", "Y", "YES"]
no = ["n", "no", "N", "NO"]
if dft != None:
dft = yes[0] if (dft in yes or dft == True) else no[0]
return ask(msg, dft=dft, vld=yes+n... | python | def ask_yesno(msg="Proceed?", dft=None):
"""Prompts the user for a yes or no answer. Returns True for yes, False
for no."""
yes = ["y", "yes", "Y", "YES"]
no = ["n", "no", "N", "NO"]
if dft != None:
dft = yes[0] if (dft in yes or dft == True) else no[0]
return ask(msg, dft=dft, vld=yes+n... | [
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jeffrimko/Qprompt | lib/qprompt.py | ask_int | def ask_int(msg="Enter an integer", dft=None, vld=None, hlp=None):
"""Prompts the user for an integer."""
vld = vld or [int]
return ask(msg, dft=dft, vld=vld, fmt=partial(cast, typ=int), hlp=hlp) | python | def ask_int(msg="Enter an integer", dft=None, vld=None, hlp=None):
"""Prompts the user for an integer."""
vld = vld or [int]
return ask(msg, dft=dft, vld=vld, fmt=partial(cast, typ=int), hlp=hlp) | [
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jeffrimko/Qprompt | lib/qprompt.py | ask_float | def ask_float(msg="Enter a float", dft=None, vld=None, hlp=None):
"""Prompts the user for a float."""
vld = vld or [float]
return ask(msg, dft=dft, vld=vld, fmt=partial(cast, typ=float), hlp=hlp) | python | def ask_float(msg="Enter a float", dft=None, vld=None, hlp=None):
"""Prompts the user for a float."""
vld = vld or [float]
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jeffrimko/Qprompt | lib/qprompt.py | ask_str | def ask_str(msg="Enter a string", dft=None, vld=None, shw=True, blk=True, hlp=None):
"""Prompts the user for a string."""
vld = vld or [str]
return ask(msg, dft=dft, vld=vld, shw=shw, blk=blk, hlp=hlp) | python | def ask_str(msg="Enter a string", dft=None, vld=None, shw=True, blk=True, hlp=None):
"""Prompts the user for a string."""
vld = vld or [str]
return ask(msg, dft=dft, vld=vld, shw=shw, blk=blk, hlp=hlp) | [
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jeffrimko/Qprompt | lib/qprompt.py | ask_captcha | def ask_captcha(length=4):
"""Prompts the user for a random string."""
captcha = "".join(random.choice(string.ascii_lowercase) for _ in range(length))
ask_str('Enter the following letters, "%s"' % (captcha), vld=[captcha, captcha.upper()], blk=False) | python | def ask_captcha(length=4):
"""Prompts the user for a random string."""
captcha = "".join(random.choice(string.ascii_lowercase) for _ in range(length))
ask_str('Enter the following letters, "%s"' % (captcha), vld=[captcha, captcha.upper()], blk=False) | [
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jeffrimko/Qprompt | lib/qprompt.py | clear | def clear():
"""Clears the console."""
if sys.platform.startswith("win"):
call("cls", shell=True)
else:
call("clear", shell=True) | python | def clear():
"""Clears the console."""
if sys.platform.startswith("win"):
call("cls", shell=True)
else:
call("clear", shell=True) | [
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jeffrimko/Qprompt | lib/qprompt.py | status | def status(*args, **kwargs):
"""Prints a status message at the start and finish of an associated
function. Can be used as a function decorator or as a function that accepts
another function as the first parameter.
**Params**:
The following parameters are available when used as a decorator:
... | python | def status(*args, **kwargs):
"""Prints a status message at the start and finish of an associated
function. Can be used as a function decorator or as a function that accepts
another function as the first parameter.
**Params**:
The following parameters are available when used as a decorator:
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jeffrimko/Qprompt | lib/qprompt.py | fatal | def fatal(msg, exitcode=1, **kwargs):
"""Prints a message then exits the program. Optionally pause before exit
with `pause=True` kwarg."""
# NOTE: Can't use normal arg named `pause` since function has same name.
pause_before_exit = kwargs.pop("pause") if "pause" in kwargs.keys() else False
echo("[FA... | python | def fatal(msg, exitcode=1, **kwargs):
"""Prints a message then exits the program. Optionally pause before exit
with `pause=True` kwarg."""
# NOTE: Can't use normal arg named `pause` since function has same name.
pause_before_exit = kwargs.pop("pause") if "pause" in kwargs.keys() else False
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jeffrimko/Qprompt | lib/qprompt.py | hrule | def hrule(width=None, char=None):
"""Outputs or returns a horizontal line of the given character and width.
Returns printed string."""
width = width or HRWIDTH
char = char or HRCHAR
return echo(getline(char, width)) | python | def hrule(width=None, char=None):
"""Outputs or returns a horizontal line of the given character and width.
Returns printed string."""
width = width or HRWIDTH
char = char or HRCHAR
return echo(getline(char, width)) | [
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jeffrimko/Qprompt | lib/qprompt.py | title | def title(msg):
"""Sets the title of the console window."""
if sys.platform.startswith("win"):
ctypes.windll.kernel32.SetConsoleTitleW(tounicode(msg)) | python | def title(msg):
"""Sets the title of the console window."""
if sys.platform.startswith("win"):
ctypes.windll.kernel32.SetConsoleTitleW(tounicode(msg)) | [
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jeffrimko/Qprompt | lib/qprompt.py | wrap | def wrap(item, args=None, krgs=None, **kwargs):
"""Wraps the given item content between horizontal lines. Item can be a
string or a function.
**Examples**:
::
qprompt.wrap("Hi, this will be wrapped.") # String item.
qprompt.wrap(myfunc, [arg1, arg2], {'krgk': krgv}) # Func item.
"... | python | def wrap(item, args=None, krgs=None, **kwargs):
"""Wraps the given item content between horizontal lines. Item can be a
string or a function.
**Examples**:
::
qprompt.wrap("Hi, this will be wrapped.") # String item.
qprompt.wrap(myfunc, [arg1, arg2], {'krgk': krgv}) # Func item.
"... | [
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jeffrimko/Qprompt | lib/qprompt.py | _guess_name | def _guess_name(desc, taken=None):
"""Attempts to guess the menu entry name from the function name."""
taken = taken or []
name = ""
# Try to find the shortest name based on the given description.
for word in desc.split():
c = word[0].lower()
if not c.isalnum():
continue
... | python | def _guess_name(desc, taken=None):
"""Attempts to guess the menu entry name from the function name."""
taken = taken or []
name = ""
# Try to find the shortest name based on the given description.
for word in desc.split():
c = word[0].lower()
if not c.isalnum():
continue
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jeffrimko/Qprompt | lib/qprompt.py | Menu.add | def add(self, name, desc, func=None, args=None, krgs=None):
"""Add a menu entry."""
self.entries.append(MenuEntry(name, desc, func, args or [], krgs or {})) | python | def add(self, name, desc, func=None, args=None, krgs=None):
"""Add a menu entry."""
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jeffrimko/Qprompt | lib/qprompt.py | Menu.enum | def enum(self, desc, func=None, args=None, krgs=None):
"""Add a menu entry whose name will be an auto indexed number."""
name = str(len(self.entries)+1)
self.entries.append(MenuEntry(name, desc, func, args or [], krgs or {})) | python | def enum(self, desc, func=None, args=None, krgs=None):
"""Add a menu entry whose name will be an auto indexed number."""
name = str(len(self.entries)+1)
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jeffrimko/Qprompt | lib/qprompt.py | Menu.show | def show(self, **kwargs):
"""Shows the menu. Any `kwargs` supplied will be passed to
`show_menu()`."""
show_kwargs = copy.deepcopy(self._show_kwargs)
show_kwargs.update(kwargs)
return show_menu(self.entries, **show_kwargs) | python | def show(self, **kwargs):
"""Shows the menu. Any `kwargs` supplied will be passed to
`show_menu()`."""
show_kwargs = copy.deepcopy(self._show_kwargs)
show_kwargs.update(kwargs)
return show_menu(self.entries, **show_kwargs) | [
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jeffrimko/Qprompt | lib/qprompt.py | Menu.run | def run(self, name):
"""Runs the function associated with the given entry `name`."""
for entry in self.entries:
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run_func(entry)
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jeffrimko/Qprompt | lib/qprompt.py | Menu.main | def main(self, auto=None, loop=False, quit=("q", "Quit"), **kwargs):
"""Runs the standard menu main logic. Any `kwargs` supplied will be
pass to `Menu.show()`. If `argv` is provided to the script, it will be
used as the `auto` parameter.
**Params**:
- auto ([str]) - If provide... | python | def main(self, auto=None, loop=False, quit=("q", "Quit"), **kwargs):
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ucsb-cs-education/hairball | hairball/plugins/initialization.py | partition_scripts | def partition_scripts(scripts, start_type1, start_type2):
"""Return two lists of scripts out of the original `scripts` list.
Scripts that begin with a `start_type1` or `start_type2` blocks
are returned first. All other scripts are returned second.
"""
match, other = [], []
for script in scrip... | python | def partition_scripts(scripts, start_type1, start_type2):
"""Return two lists of scripts out of the original `scripts` list.
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ucsb-cs-education/hairball | hairball/plugins/initialization.py | AttributeInitialization.attribute_result | def attribute_result(cls, sprites):
"""Return mapping of attributes to if they were initialized or not."""
retval = dict((x, True) for x in cls.ATTRIBUTES)
for properties in sprites.values():
for attribute, state in properties.items():
retval[attribute] &= state != cl... | python | def attribute_result(cls, sprites):
"""Return mapping of attributes to if they were initialized or not."""
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ucsb-cs-education/hairball | hairball/plugins/initialization.py | AttributeInitialization.attribute_state | def attribute_state(cls, scripts, attribute):
"""Return the state of the scripts for the given attribute.
If there is more than one 'when green flag clicked' script and they
both modify the attribute, then the attribute is considered to not be
initialized.
"""
green_fla... | python | def attribute_state(cls, scripts, attribute):
"""Return the state of the scripts for the given attribute.
If there is more than one 'when green flag clicked' script and they
both modify the attribute, then the attribute is considered to not be
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ucsb-cs-education/hairball | hairball/plugins/initialization.py | AttributeInitialization.output_results | def output_results(cls, sprites):
"""Output whether or not each attribute was correctly initialized.
Attributes that were not modified at all are considered to be properly
initialized.
"""
print(' '.join(cls.ATTRIBUTES))
format_strs = ['{{{}!s:^{}}}'.format(x, len(x)) f... | python | def output_results(cls, sprites):
"""Output whether or not each attribute was correctly initialized.
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"""
print(' '.join(cls.ATTRIBUTES))
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ucsb-cs-education/hairball | hairball/plugins/initialization.py | AttributeInitialization.sprite_changes | def sprite_changes(cls, sprite):
"""Return a mapping of attributes to their initilization state."""
retval = dict((x, cls.attribute_state(sprite.scripts, x)) for x in
(x for x in cls.ATTRIBUTES if x != 'background'))
return retval | python | def sprite_changes(cls, sprite):
"""Return a mapping of attributes to their initilization state."""
retval = dict((x, cls.attribute_state(sprite.scripts, x)) for x in
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ucsb-cs-education/hairball | hairball/plugins/initialization.py | AttributeInitialization.analyze | def analyze(self, scratch, **kwargs):
"""Run and return the results of the AttributeInitialization plugin."""
changes = dict((x.name, self.sprite_changes(x)) for x in
scratch.sprites)
changes['stage'] = {
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ucsb-cs-education/hairball | hairball/plugins/initialization.py | VariableInitialization.variable_state | def variable_state(cls, scripts, variables):
"""Return the initialization state for each variable in variables.
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parameter.
If there is more than one 'when green flag clicked' script and they
both modify the ... | python | def variable_state(cls, scripts, variables):
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ucsb-cs-education/hairball | hairball/plugins/initialization.py | VariableInitialization.analyze | def analyze(self, scratch, **kwargs):
"""Run and return the results of the VariableInitialization plugin."""
variables = dict((x, self.variable_state(x.scripts, x.variables))
for x in scratch.sprites)
variables['global'] = self.variable_state(self.iter_scripts(scratch),
... | python | def analyze(self, scratch, **kwargs):
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ucsb-cs-education/hairball | hairball/plugins/convention.py | SpriteNaming.finalize | def finalize(self):
"""Output the default sprite names found in the project."""
print('{} default sprite names found:'.format(self.total_default))
for name in self.list_default:
print(name) | python | def finalize(self):
"""Output the default sprite names found in the project."""
print('{} default sprite names found:'.format(self.total_default))
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ucsb-cs-education/hairball | hairball/plugins/convention.py | SpriteNaming.analyze | def analyze(self, scratch, **kwargs):
"""Run and return the results from the SpriteNaming plugin."""
for sprite in self.iter_sprites(scratch):
for default in self.default_names:
if default in sprite.name:
self.total_default += 1
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ramses-tech/nefertari | nefertari/tweens.py | get_tunneling | def get_tunneling(handler, registry):
""" Allows all methods to be tunneled via GET for dev/debuging
purposes.
"""
log.info('get_tunneling enabled')
def get_tunneling(request):
if request.method == 'GET':
method = request.GET.pop('_m', 'GET')
request.method = method
... | python | def get_tunneling(handler, registry):
""" Allows all methods to be tunneled via GET for dev/debuging
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"""
log.info('get_tunneling enabled')
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method = request.GET.pop('_m', 'GET')
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ramses-tech/nefertari | nefertari/tweens.py | enable_selfalias | def enable_selfalias(config, id_name):
"""
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e.g. /users/joe/account == /users/self/account if joe is in the session
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"""
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ramses-tech/nefertari | nefertari/view.py | BaseView.convert_dotted | def convert_dotted(params):
""" Convert dotted keys in :params: dictset to a nested dictset.
E.g. {'settings.foo': 'bar'} -> {'settings': {'foo': 'bar'}}
"""
if not isinstance(params, dictset):
params = dictset(params)
dotted_items = {k: v for k, v in params.items()... | python | def convert_dotted(params):
""" Convert dotted keys in :params: dictset to a nested dictset.
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ramses-tech/nefertari | nefertari/view.py | BaseView.prepare_request_params | def prepare_request_params(self, _query_params, _json_params):
""" Prepare query and update params. """
self._query_params = dictset(
_query_params or self.request.params.mixed())
self._json_params = dictset(_json_params)
ctype = self.request.content_type
if self.req... | python | def prepare_request_params(self, _query_params, _json_params):
""" Prepare query and update params. """
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ramses-tech/nefertari | nefertari/view.py | BaseView.set_override_rendered | def set_override_rendered(self):
""" Set self.request.override_renderer if needed. """
if '' in self.request.accept:
self.request.override_renderer = self._default_renderer
elif 'application/json' in self.request.accept:
self.request.override_renderer = 'nefertari_json'
... | python | def set_override_rendered(self):
""" Set self.request.override_renderer if needed. """
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ramses-tech/nefertari | nefertari/view.py | BaseView._setup_aggregation | def _setup_aggregation(self, aggregator=None):
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This makes `self.index` to first try to run aggregation and only
on fail original method is run. Method is wrapped only if it is
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ramses-tech/nefertari | nefertari/view.py | BaseView.get_collection_es | def get_collection_es(self):
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This is default implementation of querying ES collection with
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ramses-tech/nefertari | nefertari/view.py | BaseView.fill_null_values | def fill_null_values(self):
""" Fill missing model fields in JSON with {key: null value}.
Only run for PUT requests.
"""
if not self.Model:
log.info("%s has no model defined" % self.__class__.__name__)
return
empty_values = self.Model.get_null_values()
... | python | def fill_null_values(self):
""" Fill missing model fields in JSON with {key: null value}.
Only run for PUT requests.
"""
if not self.Model:
log.info("%s has no model defined" % self.__class__.__name__)
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ramses-tech/nefertari | nefertari/view.py | BaseView.set_public_limits | def set_public_limits(self):
""" Set public limits if auth is enabled and user is not
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Also sets default limit for GET, HEAD requests.
"""
if self.request.method.upper() in ['GET', 'HEAD']:
self._query_params.process_int_param('_limit', 20)
if s... | python | def set_public_limits(self):
""" Set public limits if auth is enabled and user is not
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ramses-tech/nefertari | nefertari/view.py | BaseView.convert_ids2objects | def convert_ids2objects(self):
""" Convert object IDs from `self._json_params` to objects if needed.
Only IDs that belong to relationship field of `self.Model`
are converted.
"""
if not self.Model:
log.info("%s has no model defined" % self.__class__.__name__)
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""" Convert object IDs from `self._json_params` to objects if needed.
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ramses-tech/nefertari | nefertari/view.py | BaseView.setup_default_wrappers | def setup_default_wrappers(self):
""" Setup defaulf wrappers.
Wrappers are applied when view method does not return instance
of Response. In this case nefertari renderers call wrappers and
handle response generation.
"""
# Index
self._after_calls['index'] = [
... | python | def setup_default_wrappers(self):
""" Setup defaulf wrappers.
Wrappers are applied when view method does not return instance
of Response. In this case nefertari renderers call wrappers and
handle response generation.
"""
# Index
self._after_calls['index'] = [
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turicas/mongodict | migrate_data.py | migrate_codec | def migrate_codec(config_old, config_new):
'''Migrate data from mongodict <= 0.2.1 to 0.3.0
`config_old` and `config_new` should be dictionaries with the keys
regarding to MongoDB server:
- `host`
- `port`
- `database`
- `collection`
'''
assert mongodict.__version__ i... | python | def migrate_codec(config_old, config_new):
'''Migrate data from mongodict <= 0.2.1 to 0.3.0
`config_old` and `config_new` should be dictionaries with the keys
regarding to MongoDB server:
- `host`
- `port`
- `database`
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ramses-tech/nefertari | nefertari/utils/data.py | FieldData.from_dict | def from_dict(cls, data, model):
""" Generate map of `fieldName: clsInstance` from dict.
:param data: Dict where keys are field names and values are
new values of field.
:param model: Model class to which fields from :data: belong.
"""
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""" Generate map of `fieldName: clsInstance` from dict.
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ramses-tech/nefertari | nefertari/authentication/views.py | TicketAuthViewMixin.register | def register(self):
""" Register new user by POSTing all required data. """
user, created = self.Model.create_account(
self._json_params)
if not created:
raise JHTTPConflict('Looks like you already have an account.')
self.request._user = user
pk_field = ... | python | def register(self):
""" Register new user by POSTing all required data. """
user, created = self.Model.create_account(
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raise JHTTPConflict('Looks like you already have an account.')
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ramses-tech/nefertari | nefertari/authentication/views.py | TokenAuthViewMixin.register | def register(self):
""" Register a new user by POSTing all required data.
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header.
"""
user, created = self.Model.create_account(self._json_params)
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""" Register a new user by POSTing all required data.
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ramses-tech/nefertari | nefertari/authentication/views.py | TokenAuthViewMixin.claim_token | def claim_token(self, **params):
"""Claim current token by POSTing 'login' and 'password'.
User's `Authorization` header value is returned in `WWW-Authenticate`
header.
"""
self._json_params.update(params)
success, self.user = self.Model.authenticate_by_password(
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"""Claim current token by POSTing 'login' and 'password'.
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"""
self._json_params.update(params)
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ramses-tech/nefertari | nefertari/authentication/views.py | TokenAuthViewMixin.reset_token | def reset_token(self, **params):
""" Reset current token by POSTing 'login' and 'password'.
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header.
"""
response = self.claim_token(**params)
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return response
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response = self.claim_token(**params)
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ramses-tech/nefertari | nefertari/wrappers.py | apply_privacy._apply_nested_privacy | def _apply_nested_privacy(self, data):
""" Apply privacy to nested documents.
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"""
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'drop_hidden': self.drop_hidden,
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kw = {
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'drop_hidden': self.drop_hidden,
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ramses-tech/nefertari | nefertari/wrappers.py | add_object_url._set_object_self | def _set_object_self(self, obj):
""" Add '_self' key value to :obj: dict. """
from nefertari.elasticsearch import ES
location = self.request.path_url
route_kwargs = {}
""" Check for parents """
if self.request.matchdict:
route_kwargs.update(self.request.match... | python | def _set_object_self(self, obj):
""" Add '_self' key value to :obj: dict. """
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location = self.request.path_url
route_kwargs = {}
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ramses-tech/nefertari | nefertari/resource.py | get_root_resource | def get_root_resource(config):
"""Returns the root resource."""
app_package_name = get_app_package_name(config)
return config.registry._root_resources.setdefault(
app_package_name, Resource(config)) | python | def get_root_resource(config):
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ramses-tech/nefertari | nefertari/resource.py | add_resource_routes | def add_resource_routes(config, view, member_name, collection_name, **kwargs):
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ramses-tech/nefertari | nefertari/resource.py | get_default_view_path | def get_default_view_path(resource):
"Returns the dotted path to the default view class."
parts = [a.member_name for a in resource.ancestors] +\
[resource.collection_name or resource.member_name]
if resource.prefix:
parts.insert(-1, resource.prefix)
view_file = '%s' % '_'.join(par... | python | def get_default_view_path(resource):
"Returns the dotted path to the default view class."
parts = [a.member_name for a in resource.ancestors] +\
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if resource.prefix:
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ramses-tech/nefertari | nefertari/resource.py | Resource.get_ancestors | def get_ancestors(self):
"Returns the list of ancestor resources."
if self._ancestors:
return self._ancestors
if not self.parent:
return []
obj = self.resource_map.get(self.parent.uid)
while obj and obj.member_name:
self._ancestors.append(o... | python | def get_ancestors(self):
"Returns the list of ancestor resources."
if self._ancestors:
return self._ancestors
if not self.parent:
return []
obj = self.resource_map.get(self.parent.uid)
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ramses-tech/nefertari | nefertari/resource.py | Resource.add | def add(self, member_name, collection_name='', parent=None, uid='',
**kwargs):
"""
:param member_name: singular name of the resource. It should be the
appropriate singular version of the resource given your locale
and used with members of the collection.
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**kwargs):
"""
:param member_name: singular name of the resource. It should be the
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ramses-tech/nefertari | nefertari/resource.py | Resource.add_from_child | def add_from_child(self, resource, **kwargs):
""" Add a resource with its all children resources to the current
resource.
"""
new_resource = self.add(
resource.member_name, resource.collection_name, **kwargs)
for child in resource.children:
new_resource.a... | python | def add_from_child(self, resource, **kwargs):
""" Add a resource with its all children resources to the current
resource.
"""
new_resource = self.add(
resource.member_name, resource.collection_name, **kwargs)
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opengridcc/opengrid | opengrid/datasets/datasets.py | DatasetContainer.add | def add(self, path):
"""
Add the path of a data set to the list of available sets
NOTE: a data set is assumed to be a pickled
and gzip compressed Pandas DataFrame
Parameters
----------
path : str
"""
name_with_ext = os.path.split(path)[1] # spli... | python | def add(self, path):
"""
Add the path of a data set to the list of available sets
NOTE: a data set is assumed to be a pickled
and gzip compressed Pandas DataFrame
Parameters
----------
path : str
"""
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opengridcc/opengrid | opengrid/datasets/datasets.py | DatasetContainer.unpack | def unpack(self, name):
"""
Unpacks a data set to a Pandas DataFrame
Parameters
----------
name : str
call `.list` to see all availble datasets
Returns
-------
pd.DataFrame
"""
path = self.list[name]
df = pd.read_pickl... | python | def unpack(self, name):
"""
Unpacks a data set to a Pandas DataFrame
Parameters
----------
name : str
call `.list` to see all availble datasets
Returns
-------
pd.DataFrame
"""
path = self.list[name]
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christophertbrown/bioscripts | ctbBio/sixframe.py | six_frame | def six_frame(genome, table, minimum = 10):
"""
translate each sequence into six reading frames
"""
for seq in parse_fasta(genome):
dna = Seq(seq[1].upper().replace('U', 'T'), IUPAC.ambiguous_dna)
counter = 0
for sequence in ['f', dna], ['rc', dna.reverse_complement()]:
... | python | def six_frame(genome, table, minimum = 10):
"""
translate each sequence into six reading frames
"""
for seq in parse_fasta(genome):
dna = Seq(seq[1].upper().replace('U', 'T'), IUPAC.ambiguous_dna)
counter = 0
for sequence in ['f', dna], ['rc', dna.reverse_complement()]:
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jay-johnson/network-pipeline | network_pipeline/scripts/network_agent.py | publish_processed_network_packets | def publish_processed_network_packets(
name="not-set",
task_queue=None,
result_queue=None,
need_response=False,
shutdown_msg="SHUTDOWN"):
"""
# Redis/RabbitMQ/SQS messaging endpoints for pub-sub
routing_key = ev("PUBLISH_EXCHANGE",
"reporting.acc... | python | def publish_processed_network_packets(
name="not-set",
task_queue=None,
result_queue=None,
need_response=False,
shutdown_msg="SHUTDOWN"):
"""
# Redis/RabbitMQ/SQS messaging endpoints for pub-sub
routing_key = ev("PUBLISH_EXCHANGE",
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jay-johnson/network-pipeline | network_pipeline/scripts/network_agent.py | run_main | def run_main(
need_response=False,
callback=None):
"""run_main
start the packet consumers and the packet processors
:param need_response: should send response back to publisher
:param callback: handler method
"""
stop_file = ev("STOP_FILE",
"/opt/stop_record... | python | def run_main(
need_response=False,
callback=None):
"""run_main
start the packet consumers and the packet processors
:param need_response: should send response back to publisher
:param callback: handler method
"""
stop_file = ev("STOP_FILE",
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christophertbrown/bioscripts | ctbBio/16SfromHMM.py | best_model | def best_model(seq2hmm):
"""
determine the best model: archaea, bacteria, eukarya (best score)
"""
for seq in seq2hmm:
best = []
for model in seq2hmm[seq]:
best.append([model, sorted([i[-1] for i in seq2hmm[seq][model]], reverse = True)[0]])
best_model = sorted(best, ... | python | def best_model(seq2hmm):
"""
determine the best model: archaea, bacteria, eukarya (best score)
"""
for seq in seq2hmm:
best = []
for model in seq2hmm[seq]:
best.append([model, sorted([i[-1] for i in seq2hmm[seq][model]], reverse = True)[0]])
best_model = sorted(best, ... | [
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christophertbrown/bioscripts | ctbBio/16SfromHMM.py | check_gaps | def check_gaps(matches, gap_threshold = 0):
"""
check for large gaps between alignment windows
"""
gaps = []
prev = None
for match in sorted(matches, key = itemgetter(0)):
if prev is None:
prev = match
continue
if match[0] - prev[1] >= gap_threshold:
... | python | def check_gaps(matches, gap_threshold = 0):
"""
check for large gaps between alignment windows
"""
gaps = []
prev = None
for match in sorted(matches, key = itemgetter(0)):
if prev is None:
prev = match
continue
if match[0] - prev[1] >= gap_threshold:
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christophertbrown/bioscripts | ctbBio/16SfromHMM.py | check_overlap | def check_overlap(current, hit, overlap = 200):
"""
determine if sequence has already hit the same part of the model,
indicating that this hit is for another 16S rRNA gene
"""
for prev in current:
p_coords = prev[2:4]
coords = hit[2:4]
if get_overlap(coords, p_coords) >= over... | python | def check_overlap(current, hit, overlap = 200):
"""
determine if sequence has already hit the same part of the model,
indicating that this hit is for another 16S rRNA gene
"""
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p_coords = prev[2:4]
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christophertbrown/bioscripts | ctbBio/16SfromHMM.py | check_order | def check_order(current, hit, overlap = 200):
"""
determine if hits are sequential on model and on the
same strand
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"""
prev_model = current[-1][2:4]
prev_strand = current[-1][-2]
hit_model = hit[2:4]
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# ... | python | def check_order(current, hit, overlap = 200):
"""
determine if hits are sequential on model and on the
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"""
prev_model = current[-1][2:4]
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christophertbrown/bioscripts | ctbBio/16SfromHMM.py | hit_groups | def hit_groups(hits):
"""
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* group hits for each gene
"""
groups = []
current = False
for hit in sorted(hits, key = itemgetter(0)):
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current = [hit]
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"""
* each sequence may have more than one 16S rRNA gene
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groups = []
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christophertbrown/bioscripts | ctbBio/16SfromHMM.py | find_coordinates | def find_coordinates(hmms, bit_thresh):
"""
find 16S rRNA gene sequence coordinates
"""
# get coordinates from cmsearch output
seq2hmm = parse_hmm(hmms, bit_thresh)
seq2hmm = best_model(seq2hmm)
group2hmm = {} # group2hmm[seq][group] = [model, strand, coordinates, matches, gaps]
for seq,... | python | def find_coordinates(hmms, bit_thresh):
"""
find 16S rRNA gene sequence coordinates
"""
# get coordinates from cmsearch output
seq2hmm = parse_hmm(hmms, bit_thresh)
seq2hmm = best_model(seq2hmm)
group2hmm = {} # group2hmm[seq][group] = [model, strand, coordinates, matches, gaps]
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christophertbrown/bioscripts | ctbBio/16SfromHMM.py | get_info | def get_info(line, bit_thresh):
"""
get info from either ssu-cmsearch or cmsearch output
"""
if len(line) >= 18: # output is from cmsearch
id, model, bit, inc = line[0].split()[0], line[2], float(line[14]), line[16]
sstart, send, strand = int(line[7]), int(line[8]), line[9]
mstar... | python | def get_info(line, bit_thresh):
"""
get info from either ssu-cmsearch or cmsearch output
"""
if len(line) >= 18: # output is from cmsearch
id, model, bit, inc = line[0].split()[0], line[2], float(line[14]), line[16]
sstart, send, strand = int(line[7]), int(line[8]), line[9]
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"""
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e = min(length - coords[1], buffer)
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | convert_parser_to | def convert_parser_to(parser, parser_or_type, metadata_props=None):
"""
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | get_metadata_parser | def get_metadata_parser(metadata_container, **metadata_defaults):
"""
Takes a metadata_container, which may be a type or instance of a parser, a dict, string, or file.
:return: a new instance of a parser corresponding to the standard represented by metadata_container
:see: get_parsed_content(metdata_con... | python | def get_metadata_parser(metadata_container, **metadata_defaults):
"""
Takes a metadata_container, which may be a type or instance of a parser, a dict, string, or file.
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | get_parsed_content | def get_parsed_content(metadata_content):
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1. XML string or file object: parses XML content
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-... | python | def get_parsed_content(metadata_content):
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | _import_parsers | def _import_parsers():
""" Lazy imports to prevent circular dependencies between this module and utils """
global ARCGIS_NODES
global ARCGIS_ROOTS
global ArcGISParser
global FGDC_ROOT
global FgdcParser
global ISO_ROOTS
global IsoParser
global VALID_ROOTS
if ARCGIS_NODES is N... | python | def _import_parsers():
""" Lazy imports to prevent circular dependencies between this module and utils """
global ARCGIS_NODES
global ARCGIS_ROOTS
global ArcGISParser
global FGDC_ROOT
global FgdcParser
global ISO_ROOTS
global IsoParser
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"""
Dynamically sets attributes from a Dictionary passed in by children.
The Dictionary will contain the name of each attribute as keys, and
either an XPATH mapping to a text value in _xml_tree, or a function
that takes no parameters and returns the inte... | python | def _init_metadata(self):
"""
Dynamically sets attributes from a Dictionary passed in by children.
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._init_data_map | def _init_data_map(self):
""" Default data map initialization: MUST be overridden in children """
if self._data_map is None:
self._data_map = {'_root': None}
self._data_map.update({}.fromkeys(self._metadata_props)) | python | def _init_data_map(self):
""" Default data map initialization: MUST be overridden in children """
if self._data_map is None:
self._data_map = {'_root': None}
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._get_template | def _get_template(self, root=None, **metadata_defaults):
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if self._data_map is None:
self._init_data_map()
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... | python | def _get_template(self, root=None, **metadata_defaults):
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._get_xpath_for | def _get_xpath_for(self, prop):
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xpath = self._data_map.get(prop)
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xpath = self._data_map.get(prop)
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._parse_complex | def _parse_complex(self, prop):
""" Default parsing operation for a complex struct """
xpath_root = None
xpath_map = self._data_structures[prop]
return parse_complex(self._xml_tree, xpath_root, xpath_map, prop) | python | def _parse_complex(self, prop):
""" Default parsing operation for a complex struct """
xpath_root = None
xpath_map = self._data_structures[prop]
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._parse_complex_list | def _parse_complex_list(self, prop):
""" Default parsing operation for lists of complex structs """
xpath_root = self._get_xroot_for(prop)
xpath_map = self._data_structures[prop]
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""" Default parsing operation for lists of complex structs """
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._parse_dates | def _parse_dates(self, prop=DATES):
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._update_complex | def _update_complex(self, **update_props):
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prop = update_props['prop']
xpath_root = self._get_xroot_for(prop)
xpath_map = self._data_structures[prop]
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""" Default update operation for a complex struct """
prop = update_props['prop']
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xpath_map = self._data_structures[prop]
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._update_complex_list | def _update_complex_list(self, **update_props):
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser._update_dates | def _update_dates(self, xpath_root=None, **update_props):
"""
Default update operation for Dates metadata
:see: gis_metadata.utils._complex_definitions[DATES]
"""
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prop = update_props['prop']
values = (update_props['... | python | def _update_dates(self, xpath_root=None, **update_props):
"""
Default update operation for Dates metadata
:see: gis_metadata.utils._complex_definitions[DATES]
"""
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:param use_template: if True, updates a new template XML tree; otherwise the original XML tree
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Validates instance properties, updates an XML tree with them, and writes the content to a file.
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consbio/gis-metadata-parser | gis_metadata/metadata_parser.py | MetadataParser.validate | def validate(self):
""" Default validation for updated properties: MAY be overridden in children """
validate_properties(self._data_map, self._metadata_props)
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validate_any(prop, getattr(self, prop), self._data_structures.get(prop))
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""" Default validation for updated properties: MAY be overridden in children """
validate_properties(self._data_map, self._metadata_props)
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validate_any(prop, getattr(self, prop), self._data_structures.get(prop))
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | _search_regex | def _search_regex(ops: dict, regex_pat: str):
"""
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Search order:
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | Styles.spec | def spec(self, postf_un_ops: str) -> list:
"""Return prefix unary operators list"""
spec = [(l + op, {'pat': self.pat(pat),
'postf': self.postf(r, postf_un_ops),
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for op, pat in self.styles.items()
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"""Return prefix unary operators list"""
spec = [(l + op, {'pat': self.pat(pat),
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | PrefUnGreedy.spec | def spec(self) -> list:
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | PrefUnOps.fill | def fill(self, postf_un_ops: str):
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* other styles
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* defaults
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"""
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* math styles
* other styles
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* defaults
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | PostfUnOps.one_symbol_ops_str | def one_symbol_ops_str(self) -> str:
"""Regex-escaped string with all one-symbol operators"""
return re.escape(''.join((key for key in self.ops.keys() if len(key) == 1))) | python | def one_symbol_ops_str(self) -> str:
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | SugarTeX._su_scripts_regex | def _su_scripts_regex(self):
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su_regex = (r'\\([{su_}])|([{sub}]... | python | def _su_scripts_regex(self):
"""
:return:
[compiled regex, function]
"""
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subs = re.escape(''.join([k for k in self.subscripts.keys()])) # language=PythonRegExp
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | SugarTeX._local_map | def _local_map(match, loc: str = 'lr') -> list:
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turns on/off left/right local area calculation
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"""
:param match:
:param loc: str
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turns on/off left/right local area calculation
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | SugarTeX._operators_replace | def _operators_replace(self, string: str) -> str:
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kiwi0fruit/sugartex | sugartex/sugartex_filter.py | SugarTeX.replace | def replace(self, src: str) -> str:
"""
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LaTeX string
:return: str
New LaTeX string
"""
if not self.readied:
self.ready()
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"""
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christophertbrown/bioscripts | ctbBio/strip_align.py | plot_gaps | def plot_gaps(plot, columns):
"""
plot % of gaps at each position
"""
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# plot_window([columns], len(columns)*.01, plot)
plot_window([[100 - i for i in columns]], len(columns)*.01, plot) | python | def plot_gaps(plot, columns):
"""
plot % of gaps at each position
"""
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christophertbrown/bioscripts | ctbBio/strip_align.py | strip_msa_100 | def strip_msa_100(msa, threshold, plot = False):
"""
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"""
msa = [seq for seq in parse_fasta(msa)]
columns = [[0, 0] for pos in msa[0][1]] # [[#bases, #gaps], [#bases, #gaps], ...]
for seq in msa:
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"""
strip out columns of a MSA that represent gaps for X percent (threshold) of sequences
"""
msa = [seq for seq in parse_fasta(msa)]
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smdabdoub/phylotoast | bin/extract_shared_or_unique_otuids.py | sample_group | def sample_group(sid, groups):
"""
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:type sid: str
:param sid: SampleID from dataset.
:type groups: OrderedDict
:param groups: Returned dict from phylotoast.util.gather_categories... | python | def sample_group(sid, groups):
"""
Iterate through all categories in an OrderedDict and return category name if SampleID
present in that category.
:type sid: str
:param sid: SampleID from dataset.
:type groups: OrderedDict
:param groups: Returned dict from phylotoast.util.gather_categories... | [
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smdabdoub/phylotoast | bin/extract_shared_or_unique_otuids.py | combine_sets | def combine_sets(*sets):
"""
Combine multiple sets to create a single larger set.
"""
combined = set()
for s in sets:
combined.update(s)
return combined | python | def combine_sets(*sets):
"""
Combine multiple sets to create a single larger set.
"""
combined = set()
for s in sets:
combined.update(s)
return combined | [
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smdabdoub/phylotoast | bin/extract_shared_or_unique_otuids.py | unique_otuids | def unique_otuids(groups):
"""
Get unique OTUIDs of each category.
:type groups: Dict
:param groups: {Category name: OTUIDs in category}
:return type: dict
:return: Dict keyed on category name and unique OTUIDs as values.
"""
uniques = {key: set() for key in groups}
for i, group in... | python | def unique_otuids(groups):
"""
Get unique OTUIDs of each category.
:type groups: Dict
:param groups: {Category name: OTUIDs in category}
:return type: dict
:return: Dict keyed on category name and unique OTUIDs as values.
"""
uniques = {key: set() for key in groups}
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smdabdoub/phylotoast | bin/extract_shared_or_unique_otuids.py | shared_otuids | def shared_otuids(groups):
"""
Get shared OTUIDs between all unique combinations of groups.
:type groups: Dict
:param groups: {Category name: OTUIDs in category}
:return type: dict
:return: Dict keyed on group combination and their shared OTUIDs as values.
"""
for g in sorted(groups):
... | python | def shared_otuids(groups):
"""
Get shared OTUIDs between all unique combinations of groups.
:type groups: Dict
:param groups: {Category name: OTUIDs in category}
:return type: dict
:return: Dict keyed on group combination and their shared OTUIDs as values.
"""
for g in sorted(groups):
... | [
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smdabdoub/phylotoast | bin/extract_shared_or_unique_otuids.py | write_uniques | def write_uniques(path, prefix, uniques):
"""
Given a path, the method writes out one file for each group name in the
uniques dictionary with the file name in the pattern
PATH/prefix_group.txt
with each file containing the unique OTUIDs found when comparing that group
to all the other grou... | python | def write_uniques(path, prefix, uniques):
"""
Given a path, the method writes out one file for each group name in the
uniques dictionary with the file name in the pattern
PATH/prefix_group.txt
with each file containing the unique OTUIDs found when comparing that group
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smdabdoub/phylotoast | phylotoast/util.py | storeFASTA | def storeFASTA(fastaFNH):
"""
Parse the records in a FASTA-format file by first reading the entire file into memory.
:type source: path to FAST file or open file handle
:param source: The data source from which to parse the FASTA records. Expects the
input to resolve to a collection ... | python | def storeFASTA(fastaFNH):
"""
Parse the records in a FASTA-format file by first reading the entire file into memory.
:type source: path to FAST file or open file handle
:param source: The data source from which to parse the FASTA records. Expects the
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smdabdoub/phylotoast | phylotoast/util.py | parseFASTA | def parseFASTA(fastaFNH):
"""
Parse the records in a FASTA-format file keeping the file open, and reading through
one line at a time.
:type source: path to FAST file or open file handle
:param source: The data source from which to parse the FASTA records.
Expects the input to res... | python | def parseFASTA(fastaFNH):
"""
Parse the records in a FASTA-format file keeping the file open, and reading through
one line at a time.
:type source: path to FAST file or open file handle
:param source: The data source from which to parse the FASTA records.
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smdabdoub/phylotoast | phylotoast/util.py | parse_map_file | def parse_map_file(mapFNH):
"""
Opens a QIIME mapping file and stores the contents in a dictionary keyed on SampleID
(default) or a user-supplied one. The only required fields are SampleID,
BarcodeSequence, LinkerPrimerSequence (in that order), and Description
(which must be the final field).
:... | python | def parse_map_file(mapFNH):
"""
Opens a QIIME mapping file and stores the contents in a dictionary keyed on SampleID
(default) or a user-supplied one. The only required fields are SampleID,
BarcodeSequence, LinkerPrimerSequence (in that order), and Description
(which must be the final field).
:... | [
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... | train | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L76-L108 |
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