code string | signature string | docstring string | loss_without_docstring float64 | loss_with_docstring float64 | factor float64 |
|---|---|---|---|---|---|
logger.debug("download page: %r, %r", args, kwargs)
return self.__clientDefer(downloadPage(*args, **kwargs)) | def __doDownloadPage(self, *args, **kwargs) | Works like client.downloadPage(), but handle incoming headers | 9.274728 | 8.634883 | 1.0741 |
"Verify a user's credentials."
parser = txml.Users(delegate)
return self.__downloadPage('/account/verify_credentials.xml', parser) | def verify_credentials(self, delegate=None) | Verify a user's credentials. | 26.344419 | 26.810453 | 0.982617 |
"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),
txml.parseUpdateResponse) | def update(self, status, source=None, params={}) | Update your status. Returns the ID of the new post. | 9.848126 | 6.075469 | 1.620966 |
parser = txml.Statuses(delegate)
return self.__postPage('/statuses/retweet/%s.xml' % (id), parser) | def retweet(self, id, delegate) | Retweet a post
Returns the retweet status info back to the given delegate | 16.201429 | 18.569172 | 0.872491 |
return self.__get('/statuses/friends_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | def friends(self, delegate, params={}, extra_args=None) | Get updates from friends.
Calls the delgate once for each status object received. | 10.582291 | 12.037911 | 0.87908 |
return self.__get('/statuses/home_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | def home_timeline(self, delegate, params={}, extra_args=None) | Get updates from friends.
Calls the delgate once for each status object received. | 7.569693 | 10.001319 | 0.756869 |
if user:
params['id'] = user
return self.__get('/statuses/user_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | 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. | 5.412481 | 7.040149 | 0.768802 |
"Get the most recent public timeline."
return self.__get('/statuses/public_timeline.atom', delegate, params,
extra_args=extra_args) | def public_timeline(self, delegate, params={}, extra_args=None) | Get the most recent public timeline. | 9.748096 | 7.606725 | 1.28151 |
return self.__get('/direct_messages.xml', delegate, params,
txml.Direct, extra_args=extra_args) | 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 | 10.768832 | 14.484067 | 0.743495 |
params = params.copy()
if user is not None:
params['user'] = user
if user_id is not None:
params['user_id'] = user_id
if screen_name is not None:
params['screen_name'] = screen_name
params['text'] = text
parser = txml.Direct(de... | def send_direct_message(self, text, user=None, delegate=None, screen_name=None, user_id=None, params={}) | Send a direct message | 2.812298 | 2.934687 | 0.958296 |
return self.__get('/statuses/replies.atom', delegate, params,
extra_args=extra_args) | 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. | 10.013626 | 10.771002 | 0.929684 |
parser = txml.Users(delegate)
return self.__postPage('/friendships/create/%s.xml' % (user), parser) | def follow_user(self, user, delegate) | Follow the given user.
Returns the user info back to the given delegate | 19.622629 | 25.458941 | 0.770756 |
parser = txml.Users(delegate)
return self.__postPage('/friendships/destroy/%s.xml' % (user), parser) | def unfollow_user(self, user, delegate) | Unfollow the given user.
Returns the user info back to the given delegate | 18.616955 | 23.450497 | 0.793883 |
if user:
url = '/statuses/friends/' + user + '.xml'
else:
url = '/statuses/friends.xml'
return self.__get_maybe_paging(url, delegate, params, txml.PagedUserList, extra_args, page_delegate) | 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. | 5.968116 | 6.42521 | 0.928859 |
url = '/users/show/%s.xml' % (user)
d = defer.Deferred()
self.__downloadPage(url, txml.Users(lambda u: d.callback(u))) \
.addErrback(lambda e: d.errback(e))
return d | def show_user(self, user) | Get the info for a specific user.
Returns a delegate that will receive the user in a callback. | 7.751983 | 7.091542 | 1.093131 |
if args is None:
args = {}
args['q'] = query
return self.__doDownloadPage(self.search_url + '?' + self._urlencode(args),
txml.Feed(delegate, extra_args), agent=self.agent) | 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 | 6.958767 | 8.503998 | 0.818294 |
service.Service.startService(self)
self._toState('idle')
try:
self.connect()
except NoConsumerError:
pass | 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. | 11.356627 | 10.324114 | 1.10001 |
if self._state == 'stopped':
raise Error("This service is not running. Not connecting.")
if self._state == 'connected':
if forceReconnect:
self._toState('disconnecting')
return True
else:
raise ConnectError("Alr... | 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.
@param forceReconnect: Drop an existing connection to reconnnect... | 3.621999 | 3.377448 | 1.072407 |
self._errorState = None
def cb(result):
self.protocol = None
if self._state == 'stopped':
# Don't transition to any other state. We are stopped.
pass
else:
if isinstance(result, failure.Failure):
... | 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 entries received.
The protocol, stored in L{pr... | 5.170686 | 4.950514 | 1.044475 |
def connect():
if self.noisy:
log.msg("Reconnecting now.")
self.connect()
backOff = self.backOffs[errorState]
if self._errorState != errorState or self._delay is None:
self._errorState = errorState
self._delay = backOff['... | 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. | 4.210004 | 3.713782 | 1.133616 |
try:
method = getattr(self, '_state_%s' % state)
except AttributeError:
raise ValueError("No such state %r" % state)
log.msg("%s: to state %r" % (self.__class__.__name__, state))
self._state = state
method(*args, **kwargs) | def _toState(self, state, *args, **kwargs) | Transition to the next state.
@param state: Name of the next state. | 3.158419 | 3.390367 | 0.931586 |
if self._reconnectDelayedCall:
self._reconnectDelayedCall.cancel()
self._reconnectDelayedCall = None
self.loseConnection() | 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. | 8.07396 | 6.365485 | 1.268397 |
def responseReceived(protocol):
self.makeConnection(protocol)
if self._state == 'aborting':
self._toState('disconnecting')
else:
self._toState('connected')
def trapError(failure):
self._toState('error', failure)
... | 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 transitioning to C{'disconnecting'}.
Errors wil... | 4.84985 | 4.349496 | 1.115037 |
log.err(reason)
def matchException(failure):
for errorState, backOff in self.backOffs.iteritems():
if 'errorTypes' not in backOff:
continue
if failure.check(*backOff['errorTypes']):
return errorState
... | def _state_error(self, reason) | The connection attempt resulted in an error.
Attempt a reconnect with a back-off algorithm. | 6.880278 | 6.338443 | 1.085484 |
if line and line.isdigit():
self._expectedLength = int(line)
self._rawBuffer = []
self._rawBufferLength = 0
self.setRawMode()
else:
self.keepAliveReceived() | 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. | 6.696274 | 4.021614 | 1.665071 |
self._rawBuffer.append(data)
self._rawBufferLength += len(data)
if self._rawBufferLength >= self._expectedLength:
receivedData = ''.join(self._rawBuffer)
expectedData = receivedData[:self._expectedLength]
extraData = receivedData[self._expectedLength... | 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
the remainder of the buffer. | 2.641829 | 2.131545 | 1.239396 |
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)
elif cls.COMPLEX_PROPS and name in cls.COMPLEX_PROPS:
value = cls.COMPLEX_PROPS[name].fromD... | def fromDict(cls, data) | Fill this objects attributes from a dict for known properties. | 2.002048 | 1.936767 | 1.033707 |
try:
obj = json.loads(data)
except ValueError, e:
log.err(e, 'Invalid JSON in stream: %r' % data)
return
if u'text' in obj:
obj = Status.fromDict(obj)
else:
log.msg('Unsupported object %r' % obj)
return
... | def datagramReceived(self, data) | Decode the JSON-encoded datagram and call the callback. | 4.263481 | 3.911668 | 1.089939 |
self.setTimeout(None)
if reason.check(ResponseDone, PotentialDataLoss):
self.deferred.callback(None)
else:
self.deferred.errback(reason) | 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 exceptions are treated
as error conditions. | 4.145854 | 3.376323 | 1.22792 |
def create(delegate, extra_args=None):
return listParser(list_type, delegate, extra_args)
return create | def simpleListFactory(list_type) | Used for simple parsers that support only one type of object | 10.231252 | 9.46826 | 1.080584 |
if len(namelist) > 1:
def set_sub(i):
i.setSubDelegates(namelist[1:], before, after)
self.setBeforeDelegate(namelist[0], set_sub)
elif len(namelist) == 1:
self.setDelegate(namelist[0], before, after) | def setSubDelegates(self, namelist, before=None, after=None) | Set a delegate for a sub-sub-item, according to a list of names | 2.790969 | 2.566319 | 1.087538 |
path = path.strip('/')
list_path = path.split('/')
sentinel = list_path.pop(0)
return sentinel, list_path, path | def _split_path(path) | split a path return by the api
return
- the sentinel:
- the rest of the path as a list.
- the original path stripped of / for normalisation. | 5.380266 | 3.798178 | 1.416539 |
def _wrapper_method(self, old_path, new_path):
old_path, _old_path, old_sentinel = _split_path(old_path);
new_path, _new_path, new_sentinel = _split_path(new_path);
if old_sentinel != new_sentinel:
raise ValueError('Does not know how to move thing... | def path_dispatch_rename(rename_like_method) | decorator for rename-like function, that need dispatch on 2 arguments | 4.517883 | 4.413498 | 1.023651 |
with jconfig(profile) as config:
deact = True;
if not getattr(config.NotebookApp.contents_manager_class, 'startswith',lambda x:False)('jupyterdrive'):
deact=False
if 'gdrive' not in getattr(config.NotebookApp.tornado_settings,'get', lambda _,__:'')('contents_js_source',''):
... | def deactivate(profile='default') | should be a matter of just unsetting the above keys | 5.706626 | 5.879306 | 0.970629 |
'''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 isinstance(seq, coral.RNA):
... | 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 | 3.815509 | 1.754184 | 2.175091 |
'''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
'''
pattern = restriction_enzyme... | 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 | 5.556808 | 4.371573 | 1.271123 |
'''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
:returns: 2-element list of digested sequenc... | 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
:returns: 2-element list of digested sequence, incl... | 4.456177 | 3.300551 | 1.350131 |
print(filename)
os.chdir(directory)
subprocess.Popen(["ipython", "nbconvert", "--to", "rst",
filename],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=directory) | def ipynb_to_rst(directory, filename) | Converts a given file in a directory to an rst in the same directory. | 2.934473 | 3.115523 | 0.941888 |
# 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 ".ipynb_checkpoints" not in root:
if f.endswith("ipynb"):
ipynb_to_rst(root, f) | def convert_ipynbs(directory) | Recursively converts all ipynb files in a directory into rst files in
the same directory. | 3.938568 | 3.845685 | 1.024152 |
'''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 context to use when analyzing
e... | 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 context to use when analyzing
each win... | 3.805051 | 2.917796 | 1.304084 |
'''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 bases of context to use when
analyz... | 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 bases of context to use when
analyzing each wi... | 5.52363 | 2.147151 | 2.572539 |
'''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(111)
... | def plot(self) | Plot the results of the run method. | 5.875856 | 5.378951 | 1.09238 |
'''Design primers for PCR amplifying any arbitrary sequence.
:param dna: Input sequence.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_unde... | def primers(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning', overhangs=None,
structure=False) | Design primers for PCR amplifying any arbitrary sequence.
:param dna: Input sequence.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot:... | 2.637113 | 1.30226 | 2.025028 |
'''(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.DNA
:param query_list: List of query sequences.
:type query_l... | 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.DNA
:param query_list: List of query sequences.
:type query_list: co... | 4.892581 | 2.215205 | 2.208636 |
'''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))
return report | def nonmatches(self) | Report mismatches, indels, and coverage. | 10.503677 | 6.897498 | 1.522824 |
'''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 = 0.4
# V... | def plot(self) | Make a summary plot of the alignment and highlight nonmatches. | 3.375052 | 3.12481 | 1.080082 |
'''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(result)
report = {'mismatches': [], 'ins... | def _analyze_single(self, reference, result) | Report mistmatches and indels for a single (aligned) reference and
result. | 3.62034 | 2.835608 | 1.276742 |
'''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:
self.results[i] = ... | def _remove_n(self) | Remove terminal Ns from sequencing results. | 5.11028 | 3.932151 | 1.299615 |
'''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)])) | 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 | 3.314126 | 2.221397 | 1.491911 |
'''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 cutoff - codons that
are rarer will not be used. ... | 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 cutoff - codons that
are rarer will not be used. Frequen... | 4.489327 | 1.787573 | 2.511409 |
'''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
:returns: A codon frequency table with... | 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
:returns: A codon frequency table with some c... | 3.192814 | 1.927658 | 1.656318 |
'''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 'Downloading Genome...'
han... | def fetch_genome(genome_id) | Acquire a genome from Entrez | 6.813064 | 6.542125 | 1.041414 |
'''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 concentrations: list of concentrations for primers and the
... | 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 concentrations: list of concentrations for primers and the
... | 5.043592 | 3.250504 | 1.551634 |
'''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_exts = ['.fasta', '... | 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 | 3.326115 | 2.776469 | 1.197966 |
'''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', '.abi', '.ab1']
# Exclude fi... | 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 | 3.799152 | 2.116369 | 1.795127 |
'''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.splitext(path)[1]
if e... | 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 | 3.750541 | 3.299584 | 1.136671 |
'''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 primers.
:type primer_list: coral.Primer list
:param path: A... | 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 primers.
:type primer_list: coral.Primer list
:param path: A path t... | 2.856694 | 1.650687 | 1.73061 |
'''Translate genbank feature types into usable ones (currently identical).
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 convert
:type feature_type: str
:param bio_to_coral: from ... | def _process_feature_type(feature_type, bio_to_coral=True) | Translate genbank feature types into usable ones (currently identical).
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 convert
:type feature_type: str
:param bio_to_coral: from coral t... | 4.404928 | 1.618157 | 2.722188 |
'''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 label but should still be incorpor... | def _seqfeature_to_coral(feature) | Convert a Biopython SeqFeature to a coral.Feature.
:param feature: Biopython SeqFeature
:type feature: Bio.SeqFeature | 3.583013 | 3.567224 | 1.004426 |
'''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)
sublocations = []
if feature.gaps:
# There... | def _coral_to_seqfeature(feature) | Convert a coral.Feature to a Biopython SeqFeature.
:param feature: coral Feature.
:type feature: coral.Feature | 3.572819 | 3.526821 | 1.013042 |
'''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)
for i, row_ord in enumerate(ords):
for j, col_... | 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). | 3.562066 | 2.025381 | 1.758714 |
'''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).
:type gap_open: int
:param gap_extend: The cost of extending ... | 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).
:type gap_open: int
:param gap_extend: The cost of extending an open... | 2.939344 | 1.947677 | 1.509154 |
os.chdir(directory)
process = subprocess.Popen(["make", "html"], cwd=directory)
process.communicate() | def build_docs(directory) | Builds sphinx docs from a given directory. | 3.040383 | 3.111716 | 0.977076 |
'''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
'''
binary = [int(x) for x in bin(n)[2:]]
... | 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 | 4.374403 | 2.083943 | 2.099099 |
'''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]
return ''.join([code[str(base)] for base in rever... | 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 | 3.646435 | 2.953553 | 1.234593 |
'''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
:returns: Whether the `seq` is a valid string of `material`.
:rtype: bool
:r... | 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
:returns: Whether the `seq` is a valid string of `material`.
:rtype: bool
:raises: ... | 4.965397 | 2.842016 | 1.747139 |
'''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
check_alphabet().
:rtype: str
'''
check_alphabet(seq, material)
se... | 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
check_alphabet().
:rtype: str | 5.869313 | 1.927272 | 3.045399 |
'''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 bases, can test non-ove... | 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 | 3.416863 | 2.487017 | 1.37388 |
'''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) | def copy(self) | Create a copy of the current instance.
:returns: A safely editable copy of the current sequence. | 18.710615 | 10.981757 | 1.703791 |
'''Find sequences matching a pattern.
:param pattern: Sequence for which to find matches.
:type pattern: str
:returns: Indices of pattern matches.
:rtype: list of ints
'''
if len(pattern) > len(self):
raise ValueError('Search pattern longer than sear... | def locate(self, pattern) | Find sequences matching a pattern.
:param pattern: Sequence for which to find matches.
:type pattern: str
:returns: Indices of pattern matches.
:rtype: list of ints | 4.261792 | 3.094833 | 1.377067 |
'''Return a copy of the Feature.
:returns: A safely editable copy of the current feature.
:rtype: coral.Feature
'''
return type(self)(self.name, self.start, self.stop, self.feature_type,
gene=self.gene, locus_tag=self.locus_tag,
... | def copy(self) | Return a copy of the Feature.
:returns: A safely editable copy of the current feature.
:rtype: coral.Feature | 4.888325 | 3.044854 | 1.605438 |
'''Split Nupack commands over processors.
:param inputs: List of sequences, same format as for coral.analysis.Nupack.
:type inpus: list
:param material: Input material: 'dna' or 'rna'.
:type material: str
:param cmd: Command: 'mfe', 'pairs', 'complexes', or 'concentrations'.
:type cmd: str
... | 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
:param material: Input material: 'dna' or 'rna'.
:type material: str
:param cmd: Command: 'mfe', 'pairs', 'complexes', or 'concentrations'.
:type cmd: str
:pa... | 3.821985 | 2.187514 | 1.747182 |
'''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 | 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. | 8.987692 | 3.070693 | 2.926926 |
'''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 be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param gap: Energy ... | 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 be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param gap: Energy gap within ... | 5.215931 | 1.690027 | 3.086299 |
'''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
coral.DNA or coral.RNA).
:type strand: list
:param pseudo: Enable pseu... | 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
coral.DNA or coral.RNA).
:type strand: list
:param pseudo: Enable pseudoknots.
... | 6.827022 | 2.173788 | 3.140611 |
'''Enumerates the total number of secondary structures over the
structural ensemble Ω(π) with an ordered permutation of strands. Runs
the \'count\' command.
:param strands: List of strands to use as inputs to count -multi.
:type strands: list
:param permutation: The circ... | def count_multi(self, strands, permutation=None, pseudo=False) | Enumerates the total number of secondary structures over the
structural ensemble Ω(π) with an ordered permutation of strands. Runs
the \'count\' command.
:param strands: List of strands to use as inputs to count -multi.
:type strands: list
:param permutation: The circular permut... | 5.471445 | 1.505398 | 3.634551 |
'''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
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param dotparens: The structure in d... | 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
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param dotparens: The structure in dotparens no... | 4.645195 | 1.60419 | 2.895664 |
'''Estimate the amount of time it will take to calculate all the
partition functions for each circular permutation - estimate the time
the actual \'complexes\' command will take to run.
:param strands: Strands on which to run energy. Strands must be either
coral.D... | def complexes_timeonly(self, strands, max_size) | Estimate the amount of time it will take to calculate all the
partition functions for each circular permutation - estimate the time
the actual \'complexes\' command will take to run.
:param strands: Strands on which to run energy. Strands must be either
coral.DNA or coral... | 7.573513 | 2.125971 | 3.562378 |
'''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 pfunc_multi.
:type permutation: list
... | 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 pfunc_multi.
:type permutation: list | 4.868887 | 1.907195 | 2.552905 |
'''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() | 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 | 4.243796 | 2.439801 | 1.739402 |
'''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 that represents the unpaired
... | 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 that represents the unpaired
pr... | 4.205786 | 1.639922 | 2.564625 |
'''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()
# Put on the other strand
if copy.strand =... | 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 | 3.440274 | 2.559596 | 1.344069 |
'''Open in ApE if `ApE` is in your command line path.'''
# TODO: simplify - make ApE look in PATH only
cmd = 'ApE'
if ape_path is None:
# Check for ApE in PATH
ape_executables = []
for path in os.environ['PATH'].split(os.pathsep):
exepa... | def ape(self, ape_path=None) | Open in ApE if `ApE` is in your command line path. | 3.774205 | 3.172627 | 1.189615 |
'''Create a copy of the current instance.
:returns: A safely-editable copy of the current sequence.
:rtype: coral.DNA
'''
# Significant performance improvements by skipping alphabet check
features_copy = [feature.copy() for feature in self.features]
copy = type(... | def copy(self) | Create a copy of the current instance.
:returns: A safely-editable copy of the current sequence.
:rtype: coral.DNA | 9.064727 | 5.508536 | 1.645578 |
'''Circularize linear DNA.
:returns: A circularized version of the current sequence.
:rtype: coral.DNA
'''
if self.top[-1].seq == '-' and self.bottom[0].seq == '-':
raise ValueError('Cannot circularize - termini disconnected.')
if self.bottom[-1].seq == '-' ... | def circularize(self) | Circularize linear DNA.
:returns: A circularized version of the current sequence.
:rtype: coral.DNA | 4.232485 | 3.046294 | 1.389388 |
'''Display a visualization of the sequence in an IPython notebook.'''
try:
from IPython.display import HTML
import uuid
except ImportError:
raise IPythonDisplayImportError
sequence_json = self.json()
d3cdn = '//d3js.org/d3.v3.min.js'
... | def display(self) | Display a visualization of the sequence in an IPython notebook. | 3.175673 | 2.991995 | 1.06139 |
'''Removes feature from circular plasmid and linearizes. Automatically
reorients at the base just after the feature. This operation is
complementary to the .extract() method.
:param feature_name: The feature to remove.
:type feature_name: coral.Feature
'''
rotat... | def excise(self, feature) | Removes feature from circular plasmid and linearizes. Automatically
reorients at the base just after the feature. This operation is
complementary to the .extract() method.
:param feature_name: The feature to remove.
:type feature_name: coral.Feature | 14.336 | 2.964322 | 4.836183 |
'''Extract a feature from the sequence. This operation is complementary
to the .excise() method.
:param feature: Feature object.
:type feature: coral.sequence.Feature
:param remove_subfeatures: Remove all features in the extracted
sequence asid... | def extract(self, feature, remove_subfeatures=False) | Extract a feature from the sequence. This operation is complementary
to the .excise() method.
:param feature: Feature object.
:type feature: coral.sequence.Feature
:param remove_subfeatures: Remove all features in the extracted
sequence aside from the ... | 6.147841 | 2.952086 | 2.082542 |
'''Flip the DNA - swap the top and bottom strands.
:returns: Flipped DNA (bottom strand is now top strand, etc.).
:rtype: coral.DNA
'''
copy = self.copy()
copy.top, copy.bottom = copy.bottom, copy.top
copy.features = [_flip_feature(f, len(self)) for f in copy.fe... | def flip(self) | Flip the DNA - swap the top and bottom strands.
:returns: Flipped DNA (bottom strand is now top strand, etc.).
:rtype: coral.DNA | 5.763852 | 2.830133 | 2.036601 |
'''Linearize circular DNA at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.DNA
:raises: ValueError if the input is linear DNA.
'''
if not self.circular:
... | def linearize(self, index=0) | Linearize circular DNA at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.DNA
:raises: ValueError if the input is linear DNA. | 5.914723 | 2.810955 | 2.104169 |
'''Find sequences matching a pattern. For a circular sequence, the
search extends over the origin.
:param pattern: str or NucleicAcidSequence for which to find matches.
:type pattern: str or coral.DNA
:returns: A list of top and bottom strand indices of matches.
:rtype: ... | def locate(self, pattern) | Find sequences matching a pattern. For a circular sequence, the
search extends over the origin.
:param pattern: str or NucleicAcidSequence for which to find matches.
:type pattern: str or coral.DNA
:returns: A list of top and bottom strand indices of matches.
:rtype: list of lis... | 6.700916 | 1.499176 | 4.469734 |
'''Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.DNA
:raises: ValueError if applied to linear sequence or `index` is
negative.
'''
if not... | def rotate(self, n) | Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.DNA
:raises: ValueError if applied to linear sequence or `index` is
negative. | 4.118193 | 2.456951 | 1.67614 |
'''Reverse complement the DNA.
:returns: A reverse-complemented instance of the current sequence.
:rtype: coral.DNA
'''
copy = self.copy()
# Note: if sequence is double-stranded, swapping strand is basically
# (but not entirely) the same thing - gaps affect accu... | def reverse_complement(self) | Reverse complement the DNA.
:returns: A reverse-complemented instance of the current sequence.
:rtype: coral.DNA | 10.033641 | 7.333435 | 1.368205 |
'''Select features from the features list based on feature name,
gene, or locus tag.
:param term: Search term.
:type term: str
:param by: Feature attribute to search by. Options are 'name',
'gene', and 'locus_tag'.
:type by: str
:param... | def select_features(self, term, by='name', fuzzy=False) | Select features from the features list based on feature name,
gene, or locus tag.
:param term: Search term.
:type term: str
:param by: Feature attribute to search by. Options are 'name',
'gene', and 'locus_tag'.
:type by: str
:param fuzzy: If ... | 3.213151 | 1.382727 | 2.323778 |
'''Create a feature from the current object.
:param name: Name for the new feature. Must be specified if the DNA
instance has no .name attribute.
:type name: str
:param feature_type: The type of feature (genbank standard).
:type feature_type: str
''... | def to_feature(self, name=None, feature_type='misc_feature') | Create a feature from the current object.
:param name: Name for the new feature. Must be specified if the DNA
instance has no .name attribute.
:type name: str
:param feature_type: The type of feature (genbank standard).
:type feature_type: str | 5.389203 | 2.544533 | 2.117953 |
'''Report whether the enzyme cuts outside its recognition site.
Cutting at the very end of the site returns True.
:returns: Whether the enzyme will cut outside its recognition site.
:rtype: bool
'''
for index in self.cut_site:
if index < 0 or index > len(sel... | def cuts_outside(self) | Report whether the enzyme cuts outside its recognition site.
Cutting at the very end of the site returns True.
:returns: Whether the enzyme will cut outside its recognition site.
:rtype: bool | 6.347384 | 2.640666 | 2.403706 |
'''Generate a Primer copy.
:returns: A safely-editable copy of the current primer.
:rtype: coral.DNA
'''
return type(self)(self.anneal, self.tm, overhang=self.overhang,
name=self.name, note=self.note) | def copy(self) | Generate a Primer copy.
:returns: A safely-editable copy of the current primer.
:rtype: coral.DNA | 10.951224 | 4.426711 | 2.473896 |
'''Add up nearest-neighbor parameters for a given sequence.
:param seq: DNA sequence for which to sum nearest neighbors
:type seq: str
:param pars: parameter set to use
:type pars: dict
:returns: nearest-neighbor delta_H and delta_S sums.
:rtype: tuple of floats
'''
delta0 = 0
... | def _pair_deltas(seq, pars) | Add up nearest-neighbor parameters for a given sequence.
:param seq: DNA sequence for which to sum nearest neighbors
:type seq: str
:param pars: parameter set to use
:type pars: dict
:returns: nearest-neighbor delta_H and delta_S sums.
:rtype: tuple of floats | 3.556811 | 1.778643 | 1.999734 |
'''Sum corrections for Breslauer '84 method.
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtype: list of floats
'''
deltas_corr =... | def breslauer_corrections(seq, pars_error) | Sum corrections for Breslauer '84 method.
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtype: list of floats | 3.182886 | 2.300911 | 1.383315 |
'''Sum corrections for SantaLucia '98 method (unified parameters).
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtype: list of floats
... | def santalucia98_corrections(seq, pars_error) | Sum corrections for SantaLucia '98 method (unified parameters).
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtype: list of floats | 2.92548 | 2.040009 | 1.434052 |
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