repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_code_tokens listlengths 15 672k | func_documentation_string stringlengths 1 47.2k | func_documentation_tokens listlengths 1 3.92k | split_name stringclasses 1
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.__clientDefer | def __clientDefer(self, c):
"""Return a deferred for a HTTP client, after handling incoming headers"""
def handle_headers(r):
self.gotHeaders(c.response_headers)
return r
return c.deferred.addBoth(handle_headers) | python | def __clientDefer(self, c):
"""Return a deferred for a HTTP client, after handling incoming headers"""
def handle_headers(r):
self.gotHeaders(c.response_headers)
return r
return c.deferred.addBoth(handle_headers) | [
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.__doDownloadPage | def __doDownloadPage(self, *args, **kwargs):
"""Works like client.downloadPage(), but handle incoming headers
"""
logger.debug("download page: %r, %r", args, kwargs)
return self.__clientDefer(downloadPage(*args, **kwargs)) | python | def __doDownloadPage(self, *args, **kwargs):
"""Works like client.downloadPage(), but handle incoming headers
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logger.debug("download page: %r, %r", args, kwargs)
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.verify_credentials | def verify_credentials(self, delegate=None):
"Verify a user's credentials."
parser = txml.Users(delegate)
return self.__downloadPage('/account/verify_credentials.xml', parser) | python | def verify_credentials(self, delegate=None):
"Verify a user's credentials."
parser = txml.Users(delegate)
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.update | def update(self, status, source=None, params={}):
"Update your status. Returns the ID of the new post."
params = params.copy()
params['status'] = status
if source:
params['source'] = source
return self.__parsed_post(self.__post('/statuses/update.xml', params),
... | python | def update(self, status, source=None, params={}):
"Update your status. Returns the ID of the new post."
params = params.copy()
params['status'] = status
if source:
params['source'] = source
return self.__parsed_post(self.__post('/statuses/update.xml', params),
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.retweet | def retweet(self, id, delegate):
"""Retweet a post
Returns the retweet status info back to the given delegate
"""
parser = txml.Statuses(delegate)
return self.__postPage('/statuses/retweet/%s.xml' % (id), parser) | python | def retweet(self, id, delegate):
"""Retweet a post
Returns the retweet status info back to the given delegate
"""
parser = txml.Statuses(delegate)
return self.__postPage('/statuses/retweet/%s.xml' % (id), parser) | [
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.friends | def friends(self, delegate, params={}, extra_args=None):
"""Get updates from friends.
Calls the delgate once for each status object received."""
return self.__get('/statuses/friends_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | python | def friends(self, delegate, params={}, extra_args=None):
"""Get updates from friends.
Calls the delgate once for each status object received."""
return self.__get('/statuses/friends_timeline.xml', delegate, params,
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.home_timeline | def home_timeline(self, delegate, params={}, extra_args=None):
"""Get updates from friends.
Calls the delgate once for each status object received."""
return self.__get('/statuses/home_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | python | def home_timeline(self, delegate, params={}, extra_args=None):
"""Get updates from friends.
Calls the delgate once for each status object received."""
return self.__get('/statuses/home_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | [
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.user_timeline | def user_timeline(self, delegate, user=None, params={}, extra_args=None):
"""Get the most recent updates for a user.
If no user is specified, the statuses for the authenticating user are
returned.
See search for example of how results are returned."""
if user:
param... | python | def user_timeline(self, delegate, user=None, params={}, extra_args=None):
"""Get the most recent updates for a user.
If no user is specified, the statuses for the authenticating user are
returned.
See search for example of how results are returned."""
if user:
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.public_timeline | def public_timeline(self, delegate, params={}, extra_args=None):
"Get the most recent public timeline."
return self.__get('/statuses/public_timeline.atom', delegate, params,
extra_args=extra_args) | python | def public_timeline(self, delegate, params={}, extra_args=None):
"Get the most recent public timeline."
return self.__get('/statuses/public_timeline.atom', delegate, params,
extra_args=extra_args) | [
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.direct_messages | def direct_messages(self, delegate, params={}, extra_args=None):
"""Get direct messages for the authenticating user.
Search results are returned one message at a time a DirectMessage
objects"""
return self.__get('/direct_messages.xml', delegate, params,
txml.Di... | python | def direct_messages(self, delegate, params={}, extra_args=None):
"""Get direct messages for the authenticating user.
Search results are returned one message at a time a DirectMessage
objects"""
return self.__get('/direct_messages.xml', delegate, params,
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.send_direct_message | def send_direct_message(self, text, user=None, delegate=None, screen_name=None, user_id=None, params={}):
"""Send a direct message
"""
params = params.copy()
if user is not None:
params['user'] = user
if user_id is not None:
params['user_id'] = user_id
... | python | def send_direct_message(self, text, user=None, delegate=None, screen_name=None, user_id=None, params={}):
"""Send a direct message
"""
params = params.copy()
if user is not None:
params['user'] = user
if user_id is not None:
params['user_id'] = user_id
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.replies | def replies(self, delegate, params={}, extra_args=None):
"""Get the most recent replies for the authenticating user.
See search for example of how results are returned."""
return self.__get('/statuses/replies.atom', delegate, params,
extra_args=extra_args) | python | def replies(self, delegate, params={}, extra_args=None):
"""Get the most recent replies for the authenticating user.
See search for example of how results are returned."""
return self.__get('/statuses/replies.atom', delegate, params,
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.follow_user | def follow_user(self, user, delegate):
"""Follow the given user.
Returns the user info back to the given delegate
"""
parser = txml.Users(delegate)
return self.__postPage('/friendships/create/%s.xml' % (user), parser) | python | def follow_user(self, user, delegate):
"""Follow the given user.
Returns the user info back to the given delegate
"""
parser = txml.Users(delegate)
return self.__postPage('/friendships/create/%s.xml' % (user), parser) | [
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.unfollow_user | def unfollow_user(self, user, delegate):
"""Unfollow the given user.
Returns the user info back to the given delegate
"""
parser = txml.Users(delegate)
return self.__postPage('/friendships/destroy/%s.xml' % (user), parser) | python | def unfollow_user(self, user, delegate):
"""Unfollow the given user.
Returns the user info back to the given delegate
"""
parser = txml.Users(delegate)
return self.__postPage('/friendships/destroy/%s.xml' % (user), parser) | [
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.list_friends | def list_friends(self, delegate, user=None, params={}, extra_args=None, page_delegate=None):
"""Get the list of friends for a user.
Calls the delegate with each user object found."""
if user:
url = '/statuses/friends/' + user + '.xml'
else:
url = '/statuses/frien... | python | def list_friends(self, delegate, user=None, params={}, extra_args=None, page_delegate=None):
"""Get the list of friends for a user.
Calls the delegate with each user object found."""
if user:
url = '/statuses/friends/' + user + '.xml'
else:
url = '/statuses/frien... | [
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.show_user | def show_user(self, user):
"""Get the info for a specific user.
Returns a delegate that will receive the user in a callback."""
url = '/users/show/%s.xml' % (user)
d = defer.Deferred()
self.__downloadPage(url, txml.Users(lambda u: d.callback(u))) \
.addErrback(lamb... | python | def show_user(self, user):
"""Get the info for a specific user.
Returns a delegate that will receive the user in a callback."""
url = '/users/show/%s.xml' % (user)
d = defer.Deferred()
self.__downloadPage(url, txml.Users(lambda u: d.callback(u))) \
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dustin/twitty-twister | twittytwister/twitter.py | Twitter.search | def search(self, query, delegate, args=None, extra_args=None):
"""Perform a search query.
Results are given one at a time to the delegate. An example delegate
may look like this:
def exampleDelegate(entry):
print entry.title"""
if args is None:
args = {... | python | def search(self, query, delegate, args=None, extra_args=None):
"""Perform a search query.
Results are given one at a time to the delegate. An example delegate
may look like this:
def exampleDelegate(entry):
print entry.title"""
if args is None:
args = {... | [
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dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor.startService | def startService(self):
"""
Start the service.
This causes a transition to the C{'idle'} state, and then calls
L{connect} to attempt an initial conection.
"""
service.Service.startService(self)
self._toState('idle')
try:
self.connect()
... | python | def startService(self):
"""
Start the service.
This causes a transition to the C{'idle'} state, and then calls
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"""
service.Service.startService(self)
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try:
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... | [
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dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor.connect | def connect(self, forceReconnect=False):
"""
Check current conditions and initiate connection if possible.
This is called to check preconditions for starting a new connection,
and initating the connection itself.
If the service is not running, this will do nothing.
@pa... | python | def connect(self, forceReconnect=False):
"""
Check current conditions and initiate connection if possible.
This is called to check preconditions for starting a new connection,
and initating the connection itself.
If the service is not running, this will do nothing.
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dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor.makeConnection | def makeConnection(self, protocol):
"""
Called when the connection has been established.
This method is called when an HTTP 200 response has been received,
with the protocol that decodes the individual Twitter stream elements.
That protocol will call the consumer for all Twitter... | python | def makeConnection(self, protocol):
"""
Called when the connection has been established.
This method is called when an HTTP 200 response has been received,
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dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._reconnect | def _reconnect(self, errorState):
"""
Attempt to reconnect.
If the current back-off delay is 0, L{connect} is called. Otherwise,
it will cause a transition to the C{'waiting'} state, ultimately
causing a call to L{connect} when the delay expires.
"""
def connect(... | python | def _reconnect(self, errorState):
"""
Attempt to reconnect.
If the current back-off delay is 0, L{connect} is called. Otherwise,
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dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._toState | def _toState(self, state, *args, **kwargs):
"""
Transition to the next state.
@param state: Name of the next state.
"""
try:
method = getattr(self, '_state_%s' % state)
except AttributeError:
raise ValueError("No such state %r" % state)
l... | python | def _toState(self, state, *args, **kwargs):
"""
Transition to the next state.
@param state: Name of the next state.
"""
try:
method = getattr(self, '_state_%s' % state)
except AttributeError:
raise ValueError("No such state %r" % state)
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dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._state_stopped | def _state_stopped(self):
"""
The service is not running.
This is the initial state, and the state after L{stopService} was
called. To get out of this state, call L{startService}. If there is a
current connection, we disconnect.
"""
if self._reconnectDelayedCall:... | python | def _state_stopped(self):
"""
The service is not running.
This is the initial state, and the state after L{stopService} was
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dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._state_connecting | def _state_connecting(self):
"""
A connection is being started.
A succesful attempt results in the state C{'connected'} when the
first response from Twitter has been received. Transitioning
to the state C{'aborting'} will cause an immediate disconnect instead,
by transit... | python | def _state_connecting(self):
"""
A connection is being started.
A succesful attempt results in the state C{'connected'} when the
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dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._state_error | def _state_error(self, reason):
"""
The connection attempt resulted in an error.
Attempt a reconnect with a back-off algorithm.
"""
log.err(reason)
def matchException(failure):
for errorState, backOff in self.backOffs.iteritems():
if 'errorTy... | python | def _state_error(self, reason):
"""
The connection attempt resulted in an error.
Attempt a reconnect with a back-off algorithm.
"""
log.err(reason)
def matchException(failure):
for errorState, backOff in self.backOffs.iteritems():
if 'errorTy... | [
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dustin/twitty-twister | twittytwister/streaming.py | LengthDelimitedStream.lineReceived | def lineReceived(self, line):
"""
Called when a line is received.
We expect a length in bytes or an empty line for keep-alive. If
we got a length, switch to raw mode to receive that amount of bytes.
"""
if line and line.isdigit():
self._expectedLength = int(l... | python | def lineReceived(self, line):
"""
Called when a line is received.
We expect a length in bytes or an empty line for keep-alive. If
we got a length, switch to raw mode to receive that amount of bytes.
"""
if line and line.isdigit():
self._expectedLength = int(l... | [
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dustin/twitty-twister | twittytwister/streaming.py | LengthDelimitedStream.rawDataReceived | def rawDataReceived(self, data):
"""
Called when raw data is received.
Fill the raw buffer C{_rawBuffer} until we have received at least
C{_expectedLength} bytes. Call C{datagramReceived} with the received
byte string of the expected size. Then switch back to line mode with
... | python | def rawDataReceived(self, data):
"""
Called when raw data is received.
Fill the raw buffer C{_rawBuffer} until we have received at least
C{_expectedLength} bytes. Call C{datagramReceived} with the received
byte string of the expected size. Then switch back to line mode with
... | [
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dustin/twitty-twister | twittytwister/streaming.py | TwitterObject.fromDict | def fromDict(cls, data):
"""
Fill this objects attributes from a dict for known properties.
"""
obj = cls()
obj.raw = data
for name, value in data.iteritems():
if cls.SIMPLE_PROPS and name in cls.SIMPLE_PROPS:
setattr(obj, name, value)
... | python | def fromDict(cls, data):
"""
Fill this objects attributes from a dict for known properties.
"""
obj = cls()
obj.raw = data
for name, value in data.iteritems():
if cls.SIMPLE_PROPS and name in cls.SIMPLE_PROPS:
setattr(obj, name, value)
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dustin/twitty-twister | twittytwister/streaming.py | TwitterStream.datagramReceived | def datagramReceived(self, data):
"""
Decode the JSON-encoded datagram and call the callback.
"""
try:
obj = json.loads(data)
except ValueError, e:
log.err(e, 'Invalid JSON in stream: %r' % data)
return
if u'text' in obj:
o... | python | def datagramReceived(self, data):
"""
Decode the JSON-encoded datagram and call the callback.
"""
try:
obj = json.loads(data)
except ValueError, e:
log.err(e, 'Invalid JSON in stream: %r' % data)
return
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dustin/twitty-twister | twittytwister/streaming.py | TwitterStream.connectionLost | def connectionLost(self, reason):
"""
Called when the body is complete or the connection was lost.
@note: As the body length is usually not known at the beginning of the
response we expect a L{PotentialDataLoss} when Twitter closes the
stream, instead of L{ResponseDone}. Other e... | python | def connectionLost(self, reason):
"""
Called when the body is complete or the connection was lost.
@note: As the body length is usually not known at the beginning of the
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dustin/twitty-twister | twittytwister/txml.py | simpleListFactory | def simpleListFactory(list_type):
"""Used for simple parsers that support only one type of object"""
def create(delegate, extra_args=None):
"""Create a Parser object for the specific tag type, on the fly"""
return listParser(list_type, delegate, extra_args)
return create | python | def simpleListFactory(list_type):
"""Used for simple parsers that support only one type of object"""
def create(delegate, extra_args=None):
"""Create a Parser object for the specific tag type, on the fly"""
return listParser(list_type, delegate, extra_args)
return create | [
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dustin/twitty-twister | twittytwister/txml.py | BaseXMLHandler.setSubDelegates | def setSubDelegates(self, namelist, before=None, after=None):
"""Set a delegate for a sub-sub-item, according to a list of names"""
if len(namelist) > 1:
def set_sub(i):
i.setSubDelegates(namelist[1:], before, after)
self.setBeforeDelegate(namelist[0], set_sub)
... | python | def setSubDelegates(self, namelist, before=None, after=None):
"""Set a delegate for a sub-sub-item, according to a list of names"""
if len(namelist) > 1:
def set_sub(i):
i.setSubDelegates(namelist[1:], before, after)
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jupyter/jupyter-drive | jupyterdrive/mixednbmanager.py | _split_path | def _split_path(path):
"""split a path return by the api
return
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- the rest of the path as a list.
- the original path stripped of / for normalisation.
"""
path = path.strip('/')
list_path = path.split('/')
sentinel = list_path.pop(0)
return sentinel, ... | python | def _split_path(path):
"""split a path return by the api
return
- the sentinel:
- the rest of the path as a list.
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"""
path = path.strip('/')
list_path = path.split('/')
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return sentinel, ... | [
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jupyter/jupyter-drive | jupyterdrive/mixednbmanager.py | MixedContentsManager.path_dispatch_rename | def path_dispatch_rename(rename_like_method):
"""
decorator for rename-like function, that need dispatch on 2 arguments
"""
def _wrapper_method(self, old_path, new_path):
old_path, _old_path, old_sentinel = _split_path(old_path);
new_path, _new_path, new_sentine... | python | def path_dispatch_rename(rename_like_method):
"""
decorator for rename-like function, that need dispatch on 2 arguments
"""
def _wrapper_method(self, old_path, new_path):
old_path, _old_path, old_sentinel = _split_path(old_path);
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jupyter/jupyter-drive | jupyterdrive/__init__.py | deactivate | def deactivate(profile='default'):
"""should be a matter of just unsetting the above keys
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deact = True;
if not getattr(config.NotebookApp.contents_manager_class, 'startswith',lambda x:False)('jupyterdrive'):
deact=False
if 'gdrive' not... | python | def deactivate(profile='default'):
"""should be a matter of just unsetting the above keys
"""
with jconfig(profile) as config:
deact = True;
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klavinslab/coral | coral/analysis/utils.py | sequence_type | def sequence_type(seq):
'''Validates a coral.sequence data type.
:param sequence_in: input DNA sequence.
:type sequence_in: any
:returns: The material - 'dna', 'rna', or 'peptide'.
:rtype: str
:raises: ValueError
'''
if isinstance(seq, coral.DNA):
material = 'dna'
elif isin... | python | def sequence_type(seq):
'''Validates a coral.sequence data type.
:param sequence_in: input DNA sequence.
:type sequence_in: any
:returns: The material - 'dna', 'rna', or 'peptide'.
:rtype: str
:raises: ValueError
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if isinstance(seq, coral.DNA):
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klavinslab/coral | coral/reaction/_pcr.py | pcr | def pcr(template, primer1, primer2, min_tm=50.0, min_primer_len=14):
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:param template: DNA template from which to PCR.
:type template: coral.DNA
:param primer1: First PCR primer.
:type primer1: coral.Primer
:param primer2: First PCR primer.
:type primer2: coral.Primer
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:type template: coral.DNA
:param primer1: First PCR primer.
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klavinslab/coral | coral/reaction/_restriction.py | digest | def digest(dna, restriction_enzyme):
'''Restriction endonuclease reaction.
:param dna: DNA template to digest.
:type dna: coral.DNA
:param restriction_site: Restriction site to use.
:type restriction_site: RestrictionSite
:returns: list of digested DNA fragments.
:rtype: coral.DNA list
... | python | def digest(dna, restriction_enzyme):
'''Restriction endonuclease reaction.
:param dna: DNA template to digest.
:type dna: coral.DNA
:param restriction_site: Restriction site to use.
:type restriction_site: RestrictionSite
:returns: list of digested DNA fragments.
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klavinslab/coral | coral/reaction/_restriction.py | _cut | def _cut(dna, index, restriction_enzyme):
'''Cuts template once at the specified index.
:param dna: DNA to cut
:type dna: coral.DNA
:param index: index at which to cut
:type index: int
:param restriction_enzyme: Enzyme with which to cut
:type restriction_enzyme: coral.RestrictionSite
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'''Cuts template once at the specified index.
:param dna: DNA to cut
:type dna: coral.DNA
:param index: index at which to cut
:type index: int
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klavinslab/coral | bin/ipynb2rst.py | ipynb_to_rst | def ipynb_to_rst(directory, filename):
"""Converts a given file in a directory to an rst in the same directory."""
print(filename)
os.chdir(directory)
subprocess.Popen(["ipython", "nbconvert", "--to", "rst",
filename],
stdout=subprocess.PIPE,
... | python | def ipynb_to_rst(directory, filename):
"""Converts a given file in a directory to an rst in the same directory."""
print(filename)
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subprocess.Popen(["ipython", "nbconvert", "--to", "rst",
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klavinslab/coral | bin/ipynb2rst.py | convert_ipynbs | def convert_ipynbs(directory):
"""Recursively converts all ipynb files in a directory into rst files in
the same directory."""
# The ipython_examples dir has to be in the same dir as this script
for root, subfolders, files in os.walk(os.path.abspath(directory)):
for f in files:
if ".... | python | def convert_ipynbs(directory):
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klavinslab/coral | coral/analysis/_structure/structure_windows.py | _context_walk | def _context_walk(dna, window_size, context_len, step):
'''Generate context-dependent 'non-boundedness' scores for a DNA sequence.
:param dna: Sequence to score.
:type dna: coral.DNA
:param window_size: Window size in base pairs.
:type window_size: int
:param context_len: The number of bases of... | python | def _context_walk(dna, window_size, context_len, step):
'''Generate context-dependent 'non-boundedness' scores for a DNA sequence.
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:type dna: coral.DNA
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klavinslab/coral | coral/analysis/_structure/structure_windows.py | StructureWindows.windows | def windows(self, window_size=60, context_len=90, step=10):
'''Walk through the sequence of interest in windows of window_size,
evaluate free (unbound) pair probabilities.
:param window_size: Window size in base pairs.
:type window_size: int
:param context_len: The number of bas... | python | def windows(self, window_size=60, context_len=90, step=10):
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klavinslab/coral | coral/analysis/_structure/structure_windows.py | StructureWindows.plot | def plot(self):
'''Plot the results of the run method.'''
try:
from matplotlib import pylab
except ImportError:
raise ImportError('Optional dependency matplotlib not installed.')
if self.walked:
fig = pylab.figure()
ax1 = fig.add_subplot(1... | python | def plot(self):
'''Plot the results of the run method.'''
try:
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klavinslab/coral | coral/analysis/_sequence/anneal.py | anneal | def anneal(template, primer, min_tm=50.0, min_len=10):
'''Simulates a primer binding event. Will find the maximum subset
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sequences. **Note**: Primer binding locations indicate the 3' end of the
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klavinslab/coral | coral/design/_primers.py | primer | def primer(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
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:type dna: coral.DNA
:param tm: Ideal ... | python | def primer(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
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klavinslab/coral | coral/design/_primers.py | primers | def primers(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning', overhangs=None,
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klavinslab/coral | coral/reaction/_oligo_assembly.py | assemble_oligos | def assemble_oligos(dna_list, reference=None):
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:type dna_list: coral.DNA list
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klavinslab/coral | coral/reaction/_oligo_assembly.py | bind_unique | def bind_unique(reference, query_list, min_overlap=12, right=True):
'''(5' or 3' region on reference sequence that uniquely matches the reverse
complement of the associated (5' or 3') region of one sequence in a list of
query sequences.
:param reference: Reference sequence.
:type reference: coral.D... | python | def bind_unique(reference, query_list, min_overlap=12, right=True):
'''(5' or 3' region on reference sequence that uniquely matches the reverse
complement of the associated (5' or 3') region of one sequence in a list of
query sequences.
:param reference: Reference sequence.
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klavinslab/coral | coral/analysis/_sequencing/sanger.py | Sanger.nonmatches | def nonmatches(self):
'''Report mismatches, indels, and coverage.'''
# For every result, keep a dictionary of mismatches, insertions, and
# deletions
report = []
for result in self.aligned_results:
report.append(self._analyze_single(self.aligned_reference, result))
... | python | def nonmatches(self):
'''Report mismatches, indels, and coverage.'''
# For every result, keep a dictionary of mismatches, insertions, and
# deletions
report = []
for result in self.aligned_results:
report.append(self._analyze_single(self.aligned_reference, result))
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klavinslab/coral | coral/analysis/_sequencing/sanger.py | Sanger.plot | def plot(self):
'''Make a summary plot of the alignment and highlight nonmatches.'''
import matplotlib.pyplot as plt
import matplotlib.patches as patches
# Constants to use throughout drawing
n = len(self.results)
nbases = len(self.aligned_reference)
barheight = ... | python | def plot(self):
'''Make a summary plot of the alignment and highlight nonmatches.'''
import matplotlib.pyplot as plt
import matplotlib.patches as patches
# Constants to use throughout drawing
n = len(self.results)
nbases = len(self.aligned_reference)
barheight = ... | [
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klavinslab/coral | coral/analysis/_sequencing/sanger.py | Sanger._analyze_single | def _analyze_single(self, reference, result):
'''Report mistmatches and indels for a single (aligned) reference and
result.'''
# TODO: Recalculate coverage based on reference (e.g. sequencing result
# longer than template
reference_str = str(reference)
result_str = str(re... | python | def _analyze_single(self, reference, result):
'''Report mistmatches and indels for a single (aligned) reference and
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# TODO: Recalculate coverage based on reference (e.g. sequencing result
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reference_str = str(reference)
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klavinslab/coral | coral/analysis/_sequencing/sanger.py | Sanger._remove_n | def _remove_n(self):
'''Remove terminal Ns from sequencing results.'''
for i, result in enumerate(self.results):
largest = max(str(result).split('N'), key=len)
start = result.locate(largest)[0][0]
stop = start + len(largest)
if start != stop:
... | python | def _remove_n(self):
'''Remove terminal Ns from sequencing results.'''
for i, result in enumerate(self.results):
largest = max(str(result).split('N'), key=len)
start = result.locate(largest)[0][0]
stop = start + len(largest)
if start != stop:
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klavinslab/coral | coral/design/_sequence_generation/random_sequences.py | random_dna | def random_dna(n):
'''Generate a random DNA sequence.
:param n: Output sequence length.
:type n: int
:returns: Random DNA sequence of length n.
:rtype: coral.DNA
'''
return coral.DNA(''.join([random.choice('ATGC') for i in range(n)])) | python | def random_dna(n):
'''Generate a random DNA sequence.
:param n: Output sequence length.
:type n: int
:returns: Random DNA sequence of length n.
:rtype: coral.DNA
'''
return coral.DNA(''.join([random.choice('ATGC') for i in range(n)])) | [
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:param n: Output sequence length.
:type n: int
:returns: Random DNA sequence of length n.
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klavinslab/coral | coral/design/_sequence_generation/random_sequences.py | random_codons | def random_codons(peptide, frequency_cutoff=0.0, weighted=False, table=None):
'''Generate randomized codons given a peptide sequence.
:param peptide: Peptide sequence for which to generate randomized
codons.
:type peptide: coral.Peptide
:param frequency_cutoff: Relative codon usage ... | python | def random_codons(peptide, frequency_cutoff=0.0, weighted=False, table=None):
'''Generate randomized codons given a peptide sequence.
:param peptide: Peptide sequence for which to generate randomized
codons.
:type peptide: coral.Peptide
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klavinslab/coral | coral/design/_sequence_generation/random_sequences.py | _cutoff | def _cutoff(table, frequency_cutoff):
'''Generate new codon frequency table given a mean cutoff.
:param table: codon frequency table of form {amino acid: codon: frequency}
:type table: dict
:param frequency_cutoff: value between 0 and 1.0 for mean frequency cutoff
:type frequency_cutoff: float
... | python | def _cutoff(table, frequency_cutoff):
'''Generate new codon frequency table given a mean cutoff.
:param table: codon frequency table of form {amino acid: codon: frequency}
:type table: dict
:param frequency_cutoff: value between 0 and 1.0 for mean frequency cutoff
:type frequency_cutoff: float
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klavinslab/coral | coral/database/_entrez.py | fetch_genome | def fetch_genome(genome_id):
'''Acquire a genome from Entrez
'''
# TODO: Can strandedness by found in fetched genome attributes?
# TODO: skip read/write step?
# Using a dummy email for now - does this violate NCBI guidelines?
email = 'loremipsum@gmail.com'
Entrez.email = email
print 'D... | python | def fetch_genome(genome_id):
'''Acquire a genome from Entrez
'''
# TODO: Can strandedness by found in fetched genome attributes?
# TODO: skip read/write step?
# Using a dummy email for now - does this violate NCBI guidelines?
email = 'loremipsum@gmail.com'
Entrez.email = email
print 'D... | [
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klavinslab/coral | coral/analysis/_structure/viennarna.py | ViennaRNA.cofold | def cofold(self, strand1, strand2, temp=37.0, dangles=2, nolp=False,
nogu=False, noclosinggu=False, constraints=None,
canonicalbponly=False, partition=-1, pfscale=None, gquad=False):
'''Run the RNAcofold command and retrieve the result in a dictionary.
:param strand1: Stra... | python | def cofold(self, strand1, strand2, temp=37.0, dangles=2, nolp=False,
nogu=False, noclosinggu=False, constraints=None,
canonicalbponly=False, partition=-1, pfscale=None, gquad=False):
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klavinslab/coral | coral/analysis/_structure/viennarna.py | ViennaRNA.fold | def fold(self, strand, temp=37.0, dangles=2, nolp=False, nogu=False,
noclosinggu=False, constraints=None, canonicalbponly=False,
partition=False, pfscale=None, imfeelinglucky=False, gquad=False):
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noclosinggu=False, constraints=None, canonicalbponly=False,
partition=False, pfscale=None, imfeelinglucky=False, gquad=False):
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klavinslab/coral | coral/analysis/_structure/dimers.py | dimers | def dimers(primer1, primer2, concentrations=[5e-7, 3e-11]):
'''Calculate expected fraction of primer dimers.
:param primer1: Forward primer.
:type primer1: coral.DNA
:param primer2: Reverse primer.
:type primer2: coral.DNA
:param template: DNA template.
:type template: coral.DNA
:param ... | python | def dimers(primer1, primer2, concentrations=[5e-7, 3e-11]):
'''Calculate expected fraction of primer dimers.
:param primer1: Forward primer.
:type primer1: coral.DNA
:param primer2: Reverse primer.
:type primer2: coral.DNA
:param template: DNA template.
:type template: coral.DNA
:param ... | [
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klavinslab/coral | coral/seqio/_dna.py | read_dna | def read_dna(path):
'''Read DNA from file. Uses BioPython and coerces to coral format.
:param path: Full path to input file.
:type path: str
:returns: DNA sequence.
:rtype: coral.DNA
'''
filename, ext = os.path.splitext(os.path.split(path)[-1])
genbank_exts = ['.gb', '.ape']
fasta... | python | def read_dna(path):
'''Read DNA from file. Uses BioPython and coerces to coral format.
:param path: Full path to input file.
:type path: str
:returns: DNA sequence.
:rtype: coral.DNA
'''
filename, ext = os.path.splitext(os.path.split(path)[-1])
genbank_exts = ['.gb', '.ape']
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klavinslab/coral | coral/seqio/_dna.py | read_sequencing | def read_sequencing(directory):
'''Read .seq and .abi/.ab1 results files from a dir.
:param directory: Path to directory containing sequencing files.
:type directory: str
:returns: A list of DNA sequences.
:rtype: coral.DNA list
'''
dirfiles = os.listdir(directory)
seq_exts = ['.seq', ... | python | def read_sequencing(directory):
'''Read .seq and .abi/.ab1 results files from a dir.
:param directory: Path to directory containing sequencing files.
:type directory: str
:returns: A list of DNA sequences.
:rtype: coral.DNA list
'''
dirfiles = os.listdir(directory)
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klavinslab/coral | coral/seqio/_dna.py | write_dna | def write_dna(dna, path):
'''Write DNA to a file (genbank or fasta).
:param dna: DNA sequence to write to file
:type dna: coral.DNA
:param path: file path to write. Has to be genbank or fasta file.
:type path: str
'''
# Check if path filetype is valid, remember for later
ext = os.path.... | python | def write_dna(dna, path):
'''Write DNA to a file (genbank or fasta).
:param dna: DNA sequence to write to file
:type dna: coral.DNA
:param path: file path to write. Has to be genbank or fasta file.
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klavinslab/coral | coral/seqio/_dna.py | write_primers | def write_primers(primer_list, path, names=None, notes=None):
'''Write a list of primers out to a csv file. The first three columns are
compatible with the current IDT order form (name, sequence, notes). By
default there are no notes, which is an optional parameter.
:param primer_list: A list of primer... | python | def write_primers(primer_list, path, names=None, notes=None):
'''Write a list of primers out to a csv file. The first three columns are
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klavinslab/coral | coral/seqio/_dna.py | _process_feature_type | def _process_feature_type(feature_type, bio_to_coral=True):
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The feature table is derived from the official genbank spec (gbrel.txt)
available at http://www.insdc.org/documents/feature-table
:param feature_type: feature to conver... | python | def _process_feature_type(feature_type, bio_to_coral=True):
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klavinslab/coral | coral/seqio/_dna.py | _seqfeature_to_coral | def _seqfeature_to_coral(feature):
'''Convert a Biopython SeqFeature to a coral.Feature.
:param feature: Biopython SeqFeature
:type feature: Bio.SeqFeature
'''
# Some genomic sequences don't have a label attribute
# TODO: handle genomic cases differently than others. Some features lack
# a... | python | def _seqfeature_to_coral(feature):
'''Convert a Biopython SeqFeature to a coral.Feature.
:param feature: Biopython SeqFeature
:type feature: Bio.SeqFeature
'''
# Some genomic sequences don't have a label attribute
# TODO: handle genomic cases differently than others. Some features lack
# a... | [
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klavinslab/coral | coral/seqio/_dna.py | _coral_to_seqfeature | def _coral_to_seqfeature(feature):
'''Convert a coral.Feature to a Biopython SeqFeature.
:param feature: coral Feature.
:type feature: coral.Feature
'''
bio_strand = 1 if feature.strand == 1 else -1
ftype = _process_feature_type(feature.feature_type, bio_to_coral=False)
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'''Convert a coral.Feature to a Biopython SeqFeature.
:param feature: coral Feature.
:type feature: coral.Feature
'''
bio_strand = 1 if feature.strand == 1 else -1
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klavinslab/coral | coral/analysis/_sequencing/align.py | as_ord_matrix | def as_ord_matrix(matrix, alphabet):
'''Given the SubstitutionMatrix input, generate an equivalent matrix that
is indexed by the ASCII number of each residue (e.g. A -> 65).'''
ords = [ord(c) for c in alphabet]
ord_matrix = np.zeros((max(ords) + 1, max(ords) + 1), dtype=np.integer)
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'''Given the SubstitutionMatrix input, generate an equivalent matrix that
is indexed by the ASCII number of each residue (e.g. A -> 65).'''
ords = [ord(c) for c in alphabet]
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klavinslab/coral | coral/analysis/_sequencing/align.py | aligner | def aligner(seqj, seqi, method='global', gap_open=-7, gap_extend=-7,
gap_double=-7, matrix=submat.DNA_SIMPLE.matrix,
alphabet=submat.DNA_SIMPLE.alphabet):
'''Calculates the alignment of two sequences. The global method uses
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gap_double=-7, matrix=submat.DNA_SIMPLE.matrix,
alphabet=submat.DNA_SIMPLE.alphabet):
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klavinslab/coral | coral/analysis/_sequencing/align.py | score_alignment | def score_alignment(a, b, gap_open, gap_extend, matrix):
'''Calculate the alignment score from two aligned sequences.
:param a: The first aligned sequence.
:type a: str
:param b: The second aligned sequence.
:type b: str
:param gap_open: The cost of opening a gap (negative number).
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'''Calculate the alignment score from two aligned sequences.
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:type a: str
:param b: The second aligned sequence.
:type b: str
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klavinslab/coral | bin/build_sphinx_docs.py | build_docs | def build_docs(directory):
"""Builds sphinx docs from a given directory."""
os.chdir(directory)
process = subprocess.Popen(["make", "html"], cwd=directory)
process.communicate() | python | def build_docs(directory):
"""Builds sphinx docs from a given directory."""
os.chdir(directory)
process = subprocess.Popen(["make", "html"], cwd=directory)
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klavinslab/coral | coral/design/_gibson.py | gibson_primers | def gibson_primers(dna1, dna2, overlap='mixed', maxlen=80, overlap_tm=65.0,
insert=None, primer_kwargs=None):
'''Design Gibson primers given two DNA sequences (connect left to right)
:param dna1: First piece of DNA for which to design primers. Once Gibsoned,
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:param seq_list: List of DNA sequences to stitch together
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klavinslab/coral | coral/sequence/_sequence.py | _decompose | def _decompose(string, n):
'''Given string and multiplier n, find m**2 decomposition.
:param string: input string
:type string: str
:param n: multiplier
:type n: int
:returns: generator that produces m**2 * string if m**2 is a factor of n
:rtype: generator of 0 or 1
'''
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:param string: input string
:type string: str
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:type n: int
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klavinslab/coral | coral/sequence/_sequence.py | reverse_complement | def reverse_complement(sequence, material):
'''Reverse complement a sequence.
:param sequence: Sequence to reverse complement
:type sequence: str
:param material: dna, rna, or peptide.
:type material: str
'''
code = dict(COMPLEMENTS[material])
reverse_sequence = sequence[::-1]
retur... | python | def reverse_complement(sequence, material):
'''Reverse complement a sequence.
:param sequence: Sequence to reverse complement
:type sequence: str
:param material: dna, rna, or peptide.
:type material: str
'''
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klavinslab/coral | coral/sequence/_sequence.py | check_alphabet | def check_alphabet(seq, material):
'''Verify that a given string is valid DNA, RNA, or peptide characters.
:param seq: DNA, RNA, or peptide sequence.
:type seq: str
:param material: Input material - 'dna', 'rna', or 'pepide'.
:type sequence: str
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:type seq: str
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klavinslab/coral | coral/sequence/_sequence.py | process_seq | def process_seq(seq, material):
'''Validate and process sequence inputs.
:param seq: input sequence
:type seq: str
:param material: DNA, RNA, or peptide
:type: str
:returns: Uppercase version of `seq` with the alphabet checked by
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:rtype: str
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'''Validate and process sequence inputs.
:param seq: input sequence
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klavinslab/coral | coral/sequence/_sequence.py | palindrome | def palindrome(seq):
'''Test whether a sequence is palindrome.
:param seq: Sequence to analyze (DNA or RNA).
:type seq: coral.DNA or coral.RNA
:returns: Whether a sequence is a palindrome.
:rtype: bool
'''
seq_len = len(seq)
if seq_len % 2 == 0:
# Sequence has even number of ba... | python | def palindrome(seq):
'''Test whether a sequence is palindrome.
:param seq: Sequence to analyze (DNA or RNA).
:type seq: coral.DNA or coral.RNA
:returns: Whether a sequence is a palindrome.
:rtype: bool
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klavinslab/coral | coral/sequence/_sequence.py | Sequence.copy | def copy(self):
'''Create a copy of the current instance.
:returns: A safely editable copy of the current sequence.
'''
# Significant performance improvements by skipping alphabet check
return type(self)(self.seq, self.material, run_checks=False) | python | def copy(self):
'''Create a copy of the current instance.
:returns: A safely editable copy of the current sequence.
'''
# Significant performance improvements by skipping alphabet check
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klavinslab/coral | coral/sequence/_sequence.py | Sequence.locate | def locate(self, pattern):
'''Find sequences matching a pattern.
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:type pattern: str
:returns: Indices of pattern matches.
:rtype: list of ints
'''
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'''Find sequences matching a pattern.
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klavinslab/coral | coral/analysis/_structure/nupack.py | nupack_multi | def nupack_multi(seqs, material, cmd, arguments, report=True):
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:type inpus: list
:param material: Input material: 'dna' or 'rna'.
:type material: str
:param cmd: Command: 'mfe',... | python | def nupack_multi(seqs, material, cmd, arguments, report=True):
'''Split Nupack commands over processors.
:param inputs: List of sequences, same format as for coral.analysis.Nupack.
:type inpus: list
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klavinslab/coral | coral/analysis/_structure/nupack.py | run_nupack | def run_nupack(kwargs):
'''Run picklable Nupack command.
:param kwargs: keyword arguments to pass to Nupack as well as 'cmd'.
:returns: Variable - whatever `cmd` returns.
'''
run = NUPACK(kwargs['seq'])
output = getattr(run, kwargs['cmd'])(**kwargs['arguments'])
return output | python | def run_nupack(kwargs):
'''Run picklable Nupack command.
:param kwargs: keyword arguments to pass to Nupack as well as 'cmd'.
:returns: Variable - whatever `cmd` returns.
'''
run = NUPACK(kwargs['seq'])
output = getattr(run, kwargs['cmd'])(**kwargs['arguments'])
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.pfunc_multi | def pfunc_multi(self, strands, permutation=None, temp=37.0, pseudo=False,
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'''Compute the partition function for an ordered complex of strands.
Runs the \'pfunc\' command.
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.pairs | def pairs(self, strand, cutoff=0.001, temp=37.0, pseudo=False,
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Runs the \'pairs\' command.
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.pairs_multi | def pairs_multi(self, strands, cutoff=0.001, permutation=None, temp=37.0,
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magnesium=0.0):
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.mfe | def mfe(self, strand, degenerate=False, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the MFE for an ordered complex of strands. Runs the \'mfe\'
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:param strand: Strand on which to run mfe. Strands must be either
... | python | def mfe(self, strand, degenerate=False, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.mfe_multi | def mfe_multi(self, strands, permutation=None, degenerate=False, temp=37.0,
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magnesium=0.0):
'''Compute the MFE for an ordered complex of strands. Runs the \'mfe\'
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:param strands: Strands on whi... | python | def mfe_multi(self, strands, permutation=None, degenerate=False, temp=37.0,
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.subopt | def subopt(self, strand, gap, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the suboptimal structures within a defined energy gap of the
MFE. Runs the \'subopt\' command.
:param strand: Strand on which to run subopt. Strands must b... | python | def subopt(self, strand, gap, temp=37.0, pseudo=False, material=None,
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.count | def count(self, strand, pseudo=False):
'''Enumerates the total number of secondary structures over the
structural ensemble Ω(π). Runs the \'count\' command.
:param strand: Strand on which to run count. Strands must be either
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:type strand: ... | python | def count(self, strand, pseudo=False):
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.count_multi | def count_multi(self, strands, permutation=None, pseudo=False):
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.energy | def energy(self, strand, dotparens, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Calculate the free energy of a given sequence structure. Runs the
\'energy\' command.
:param strand: Strand on which to run energy. Strands must be either
... | python | def energy(self, strand, dotparens, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Calculate the free energy of a given sequence structure. Runs the
\'energy\' command.
:param strand: Strand on which to run energy. Strands must be either
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.complexes | def complexes(self, strands, max_size, ordered=False, pairs=False,
mfe=False, cutoff=0.001, degenerate=False, temp=37.0,
pseudo=False, material=None, dangles='some', sodium=1.0,
magnesium=0.0):
'''
:param strands: Strands on which to run energy. Stra... | python | def complexes(self, strands, max_size, ordered=False, pairs=False,
mfe=False, cutoff=0.001, degenerate=False, temp=37.0,
pseudo=False, material=None, dangles='some', sodium=1.0,
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.complexes_timeonly | def complexes_timeonly(self, strands, max_size):
'''Estimate the amount of time it will take to calculate all the
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:param strands: Strands on which to run energy. Stra... | python | def complexes_timeonly(self, strands, max_size):
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.concentrations | def concentrations(self, complexes, concs, ordered=False, pairs=False,
cutoff=0.001, temp=37.0):
'''
:param complexes: A list of the type returned by the complexes()
method.
:type complexes: list
:param concs: The concentration(s) of each ... | python | def concentrations(self, complexes, concs, ordered=False, pairs=False,
cutoff=0.001, temp=37.0):
'''
:param complexes: A list of the type returned by the complexes()
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:type complexes: list
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.distributions | def distributions(self, complexes, counts, volume, maxstates=1e7,
ordered=False, temp=37.0):
'''Runs the \'distributions\' NUPACK command. Note: this is intended
for a relatively small number of species (on the order of ~20
total strands for complex size ~14).
:par... | python | def distributions(self, complexes, counts, volume, maxstates=1e7,
ordered=False, temp=37.0):
'''Runs the \'distributions\' NUPACK command. Note: this is intended
for a relatively small number of species (on the order of ~20
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:par... | [
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK._multi_lines | def _multi_lines(self, strands, permutation):
'''Prepares lines to write to file for pfunc command input.
:param strand: Strand input (cr.DNA or cr.RNA).
:type strand: cr.DNA or cr.DNA
:param permutation: Permutation (e.g. [1, 2, 3, 4]) of the type used
by pf... | python | def _multi_lines(self, strands, permutation):
'''Prepares lines to write to file for pfunc command input.
:param strand: Strand input (cr.DNA or cr.RNA).
:type strand: cr.DNA or cr.DNA
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK._read_tempfile | def _read_tempfile(self, filename):
'''Read in and return file that's in the tempdir.
:param filename: Name of the file to read.
:type filename: str
'''
with open(os.path.join(self._tempdir, filename)) as f:
return f.read() | python | def _read_tempfile(self, filename):
'''Read in and return file that's in the tempdir.
:param filename: Name of the file to read.
:type filename: str
'''
with open(os.path.join(self._tempdir, filename)) as f:
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klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK._pairs_to_np | def _pairs_to_np(self, pairlist, dim):
'''Given a set of pair probability lines, construct a numpy array.
:param pairlist: a list of pair probability triples
:type pairlist: list
:returns: An upper triangular matrix of pair probabilities augmented
with one extra column... | python | def _pairs_to_np(self, pairlist, dim):
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:param pairlist: a list of pair probability triples
:type pairlist: list
:returns: An upper triangular matrix of pair probabilities augmented
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klavinslab/coral | coral/sequence/_dna.py | _flip_feature | def _flip_feature(self, feature, parent_len):
'''Adjust a feature's location when flipping DNA.
:param feature: The feature to flip.
:type feature: coral.Feature
:param parent_len: The length of the sequence to which the feature belongs.
:type parent_len: int
'''
copy = feature.copy()
... | python | def _flip_feature(self, feature, parent_len):
'''Adjust a feature's location when flipping DNA.
:param feature: The feature to flip.
:type feature: coral.Feature
:param parent_len: The length of the sequence to which the feature belongs.
:type parent_len: int
'''
copy = feature.copy()
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