JorgeVB/code_unlearning_dataset · Data Studio

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Invoke the `UpdateItem`_ function. Edits an existing item's attributes, or adds a new item to the table if it does not already exist. You can put, delete, or add attribute values. You can also perform a conditional update on an existing item (insert a new attribute name-value pair if it...
A `Query`_ operation uses the primary key of a table or a secondary index to directly access items from that table or index. :param str table_name: The name of the table containing the requested items. :param bool consistent_read: Determines the read consistency model: If ...
The `Scan`_ operation returns one or more items and item attributes by accessing every item in a table or a secondary index. If the total number of scanned items exceeds the maximum data set size limit of 1 MB, the scan stops and results are returned to the user as a ``LastEvaluatedKey`...
Execute a DynamoDB action with the given parameters. The method will retry requests that failed due to OS level errors or when being throttled by DynamoDB. :param str action: DynamoDB action to invoke :param dict parameters: parameters to send into the action :rtype: tornado.con...
Assign a method to invoke when a request has encountered an unrecoverable error in an action execution. :param method callback: The method to invoke def set_error_callback(self, callback): """Assign a method to invoke when a request has encountered an unrecoverable error in an action e...
Assign a method to invoke when a request has completed gathering measurements. :param method callback: The method to invoke def set_instrumentation_callback(self, callback): """Assign a method to invoke when a request has completed gathering measurements. :param method callbac...
Invoke a DynamoDB action :param str action: DynamoDB action to invoke :param dict parameters: parameters to send into the action :param int attempt: Which attempt number this is :param list measurements: A list for accumulating request measurements :rtype: tornado.concurrent.Fut...
Invoked when the HTTP request to the DynamoDB has returned and is responsible for setting the future result or exception based upon the HTTP response provided. :param str action: The action that was taken :param str table: The table name the action was made against :param int at...
Process the raw AWS response, returning either the mapped exception or deserialized response. :param tornado.concurrent.Future response: The request future :rtype: dict or list :raises: sprockets_dynamodb.exceptions.DynamoDBException def _process_response(response): """Process...
Write and obj in bdb. :param obj: value to be written in bdb. :param resource_id: id to make possible read and search for an resource. :return: id of the transaction def write(self, obj, resource_id=None): """Write and obj in bdb. :param obj: value to be written in bdb. ...
Read and obj in bdb using the tx_id. :param resource_id: id of the transaction to be read. :return: value with the data, transaction id and transaction. def _get(self, tx_id): """Read and obj in bdb using the tx_id. :param resource_id: id of the transaction to be read. :return...
Update and obj in bdb using the tx_id. :param metadata: new metadata for the transaction. :param tx_id: id of the transaction to be updated. :return: id of the transaction. def _update(self, metadata, tx_id, resource_id): """Update and obj in bdb using the tx_id. :param metada...
List all the objects saved in the namespace. :param search_from: TBI :param search_to: TBI :param offset: TBI :param limit: max number of values to be shows. :return: list with transactions. def list(self, search_from=None, search_to=None, limit=None): """List all ...
List all the objects saved in the namespace. :param search_from: TBI :param search_to: TBI :param offset: TBI :param limit: max number of values to be shows. :return: list with transactions. def _list(self): """List all the objects saved in the namespace. :para...
Query to bdb namespace. :param query_string: query in string format. :return: list of transactions that match with the query. def query(self, search_model: QueryModel): """Query to bdb namespace. :param query_string: query in string format. :return: list of transactions that m...
Delete a transaction. Read documentation about CRAB model in https://blog.bigchaindb.com/crab-create-retrieve-append-burn-b9f6d111f460. :param tx_id: transaction id :return: def _delete(self, tx_id): """Delete a transaction. Read documentation about CRAB model in https://blog.bigchaindb.com/cr...
Return the tx_id of the first transaction. :param tx_id: Transaction id to start the recursive search. :return Transaction id parent. def get_asset_id(self, tx_id): """Return the tx_id of the first transaction. :param tx_id: Transaction id to start the recursive search. :retur...
write ENVI header files Parameters ---------- data: str or dict the file or dictionary to get the info from filename: str the HDR file to write Returns ------- def hdr(data, filename): """ write ENVI header files Parameters ---------- data: str or dict ...
read a HDR file into a dictionary http://gis.stackexchange.com/questions/48618/how-to-read-write-envi-metadata-using-gdal Returns ------- dict the hdr file metadata attributes def __hdr2dict(self): """ read a HDR file into a dictionary http://gis.stac...
write object to an ENVI header file def write(self, filename='same'): """ write object to an ENVI header file """ if filename == 'same': filename = self.filename if not filename.endswith('.hdr'): filename += '.hdr' with open(filename, 'w') as out:...
Setup of maximum speed def MaxSpeed(self, speed): ' Setup of maximum speed ' spi.SPI_write_byte(self.CS, 0x07) # Max Speed setup spi.SPI_write_byte(self.CS, 0x00) spi.SPI_write_byte(self.CS, speed)
Go to Zero position def GoZero(self, speed): ' Go to Zero position ' self.ReleaseSW() spi.SPI_write_byte(self.CS, 0x82 \| (self.Dir & 1)) # Go to Zero spi.SPI_write_byte(self.CS, 0x00) spi.SPI_write_byte(self.CS, speed) while self.IsBusy(): pass ...
Move some distance units from current position def Move(self, units): ' Move some distance units from current position ' steps = units * self.SPU # translate units to steps if steps > 0: # look for direction spi.SPI_write_byte(self.CS, 0x40...
Report given status bit def ReadStatusBit(self, bit): ' Report given status bit ' spi.SPI_write_byte(self.CS, 0x39) # Read from address 0x19 (STATUS) spi.SPI_write_byte(self.CS, 0x00) data0 = spi.SPI_read_byte() # 1st byte spi.SPI_write_byte(self.CS, 0x00) da...
Writes a data to a SPI device selected by chipselect bit. def SPI_write_byte(self, chip_select, data): 'Writes a data to a SPI device selected by chipselect bit. ' self.bus.write_byte_data(self.address, chip_select, data)
Writes data to SPI device selected by chipselect bit. def SPI_write(self, chip_select, data): 'Writes data to SPI device selected by chipselect bit. ' dat = list(data) dat.insert(0, chip_select) return self.bus.write_i2c_block(self.address, dat);
Configure SPI interface parameters. def SPI_config(self,config): 'Configure SPI interface parameters.' self.bus.write_byte_data(self.address, 0xF0, config) return self.bus.read_byte_data(self.address, 0xF0)
Reads logic state on GPIO enabled slave-selects pins. def GPIO_read(self): 'Reads logic state on GPIO enabled slave-selects pins.' self.bus.write_byte_data(self.address, 0xF5, 0x0f) status = self.bus.read_byte(self.address) bits_values = dict([('SS0',status & 0x01 == 0x01),('SS1',status...
Enable or disable slave-select pins as gpio. def GPIO_config(self, gpio_enable, gpio_config): 'Enable or disable slave-select pins as gpio.' self.bus.write_byte_data(self.address, 0xF6, gpio_enable) self.bus.write_byte_data(self.address, 0xF7, gpio_config) return
Returns sensors I2C address. def get_address(self): """ Returns sensors I2C address. """ LOGGER.debug("Reading RPS01A sensor's address.",) return self.bus.read_byte_data(self.address, self.address_reg)
Returns programmed zero position in OTP memory. def get_zero_position(self): """ Returns programmed zero position in OTP memory. """ LSB = self.bus.read_byte_data(self.address, self.zero_position_MSB) MSB = self.bus.read_byte_data(self.address, self.zero_position_LSB) D...
Returns sensor's Automatic Gain Control actual value. 0 - Represents high magtetic field 0xFF - Represents low magnetic field def get_agc_value(self): """ Returns sensor's Automatic Gain Control actual value. 0 - Represents high magtetic field 0xFF...
Reads diagnostic data from the sensor. OCF (Offset Compensation Finished) - logic high indicates the finished Offset Compensation Algorithm. After power up the flag remains always to logic high. COF (Cordic Overflow) - logic high indicates an out of range error in the CORDIC part. When this bit is set,...
Retuns measured angle in degrees in range 0-360. def get_angle(self, verify = False): """ Retuns measured angle in degrees in range 0-360. """ LSB = self.bus.read_byte_data(self.address, self.angle_LSB) MSB = self.bus.read_byte_data(self.address, self.angle_MSB) DATA = (...
Annotating BED file based on reference features annotations. def main(input_bed, output_file, output_features=False, genome=None, only_canonical=False, short=False, extended=False, high_confidence=False, ambiguities_method=False, coding_only=False, collapse_exons=False, work_dir=False, is_debug=False...
% of Full Charge def StateOfCharge(self): """ % of Full Charge """ return (self.bus.read_byte_data(self.address, 0x02) + self.bus.read_byte_data(self.address, 0x03) * 256)
Get cells chemistry def Chemistry(self): ''' Get cells chemistry ''' length = self.bus.read_byte_data(self.address, 0x79) chem = [] for n in range(length): chem.append(self.bus.read_byte_data(self.address, 0x7A + n)) return chem
r"""(slow) 2D reconstruction with the Fourier diffraction theorem Two-dimensional diffraction tomography reconstruction algorithm for scattering of a plane wave :math:`u_0(\mathbf{r}) = u_0(x,z)` by a dielectric object with refractive index :math:`n(x,z)`. This function implements the solution...
r"""2D backpropagation with the Fourier diffraction theorem Two-dimensional diffraction tomography reconstruction algorithm for scattering of a plane wave :math:`u_0(\mathbf{r}) = u_0(x,z)` by a dielectric object with refractive index :math:`n(x,z)`. This method implements the 2D backpropagati...
triangles. Colors: - http://paletton.com/#uid=70l150klllletuehUpNoMgTsdcs shade 2 def color(x, y): """triangles. Colors: - http://paletton.com/#uid=70l150klllletuehUpNoMgTsdcs shade 2 """ if (x-4) > (y-4) and -(y-4) <= (x-4): # right return "#CDB95B" elif (x-4) > (y-4...
Reads data from desired register only once. def single_read(self, register): ''' Reads data from desired register only once. ''' comm_reg = (0b00010 << 3) + register if register == self.AD7730_STATUS_REG: bytes_num = 1 elif register == self.AD7730_...
RDY - Ready Bit. This bit provides the status of the RDY flag from the part. The status and function of this bit is the same as the RDY output pin. A number of events set the RDY bit high as indicated in Table XVIII in datasheet STDY - Steady Bit. This bit is updated when the filter writes a result to the Data...
def setMode(self ,mode = self.AD7730_IDLE_MODE ,polarity = self.AD7730_UNIPOLAR_MODE ,den = self.AD7730_IODISABLE_MODE ,iovalue = 0b00 ,data_lenght = self.AD7730_24bitDATA_MODE ,reference = self.AD77...
get N random headers from a fastq file without reading the whole thing into memory modified from: http://www.biostars.org/p/6544/ def downsample(work_dir, sample_name, fastq_left_fpath, fastq_right_fpath, downsample_to, num_pairs=None): """ get N random headers from a fastq file without reading the who...
The physical value RH given above corresponds to the relative humidity above liquid water according to World Meteorological Organization (WMO) def get_hum(self, raw = False): """ The physical value RH given above corresponds to the relative humidity above liquid water according ...
4.12 Checksum Calculation from an unsigned short input def _calculate_checksum(value): """4.12 Checksum Calculation from an unsigned short input""" # CRC polynomial = 0x131 # //P(x)=x^8+x^5+x^4+1 = 100110001 crc = 0xFF # calculates 8-Bit checksum with given polynomial ...
Run when button is pressed. def run(self): """Run when button is pressed.""" inside = 0 for draws in range(1, self.data['samples']): # generate points and check whether they are inside the unit circle r1, r2 = (random(), random()) if r1 2 + r2 2 < 1.0:...
Decorator for action handlers. The action name is inferred from the function name. This also decorates the method with `tornado.gen.coroutine` so that `~tornado.concurrent.Future` can be yielded. def on(f): """Decorator for action handlers. The action name is inferred from the function name. ...
Decorator for action handlers. :param str action: explicit action name This also decorates the method with `tornado.gen.coroutine` so that `~tornado.concurrent.Future` can be yielded. def on_action(action): """Decorator for action handlers. :param str action: explicit action name This also ...
Initialize datastores for this analysis instance. This creates instances of :class:`.Datastore` at ``data`` and ``class_data`` with the datastore domains being the current id and the class name of this analysis respectively. Overwrite this method to use other datastore backends. def i...
Emit a signal to the frontend. :param str signal: name of the signal :param message: message to send :returns: return value from frontend emit function :rtype: tornado.concurrent.Future def emit(self, signal, message='__nomessagetoken__'): """Emit a signal to the frontend. ...
Set value at position i and return a Future. :rtype: tornado.concurrent.Future def set(self, i, value): """Set value at position i and return a Future. :rtype: tornado.concurrent.Future """ value_encoded = encode(value, self.get_change_trigger(i)) if i in self.data an...
Set a value at key and return a Future. :rtype: tornado.concurrent.Future def set(self, key, value): """Set a value at key and return a Future. :rtype: tornado.concurrent.Future """ value_encoded = encode(value, self.get_change_trigger(key)) if key in self.data and se...
Update. def update(self, new_data): """Update.""" for k, v in new_data.items(): self[k] = v return self
Trigger all callbacks that were set with on_change(). def trigger_all_change_callbacks(self): """Trigger all callbacks that were set with on_change().""" return [ ret for key in DatastoreLegacy.store[self.domain].keys() for ret in self.trigger_change_callbacks(key) ...
Set value at key and return a Future :rtype: tornado.concurrent.Future def set(self, key, value): """Set value at key and return a Future :rtype: tornado.concurrent.Future """ return DatastoreLegacy.store[self.domain].set(key, value)
Initialize datastore. Only sets values for keys that are not in the datastore already. :param dict key_value_pairs: A set of key value pairs to use to initialize the datastore. def init(self, key_value_pairs): """Initialize datastore. Only sets values for keys that are no...
Close and delete instance. def close(self): """Close and delete instance.""" # remove callbacks DatastoreLegacy.datastores[self.domain].remove(self) # delete data after the last instance is gone if self.release_storage and \ not DatastoreLegacy.datastores[self.domai...
Recursively add the current index (with respect to a repeated section) in all data dictionaries. def AddIndex(node, index=None): """ Recursively add the current index (with respect to a repeated section) in all data dictionaries. """ if isinstance(node, list): for i, item in enumerate(node): AddI...
Renerate documentation when it changes. def watch(): """Renerate documentation when it changes.""" # Start with a clean build sphinx_build['-b', 'html', '-E', 'docs', 'docs/_build/html'] & FG handler = ShellCommandTrick( shell_command='sphinx-build -b html docs docs/_build/html', patt...
Generate html and dirhtml output. def gen(skipdirhtml=False): """Generate html and dirhtml output.""" docs_changelog = 'docs/changelog.rst' check_git_unchanged(docs_changelog) pandoc('--from=markdown', '--to=rst', '--output=' + docs_changelog, 'CHANGELOG.md') if not skipdirhtml: sphinx_buil...
redraw the cross-hair on the horizontal slice plot Parameters ---------- x: int the x image coordinate y: int the y image coordinate Returns ------- def __reset_crosshair(self): """ redraw the cross-hair on the horizontal slice p...
set up the vertical profile plot Returns ------- def __init_vertical_plot(self): """ set up the vertical profile plot Returns ------- """ # clear the plot if lines have already been drawn on it if len(self.ax2.lines) > 0: self.ax2.cl...
respond to mouse clicks in the plot. This function responds to clicks on the first (horizontal slice) plot and updates the vertical profile and slice plots Parameters ---------- event: matplotlib.backend_bases.MouseEvent the click event object containing image coordi...
Returns a function suitable for passing as the more_formatters argument to Template. NOTE: In Java, this would be implemented using the 'Composite' pattern. A list of formatter lookup function behaves the same as a single formatter lookup funcion. Note the distinction between formatter lookup funct...
Use Python % format strings as template format specifiers. def PythonPercentFormat(format_str): """Use Python % format strings as template format specifiers.""" if format_str.startswith('printf '): fmt = format_str[len('printf '):] return lambda value: fmt % value else: return None
Returns whether the value should be considered a plural value. Integers greater than 1 are plural, and lists with length greater than one are too. def Plural(format_str): """Returns whether the value should be considered a plural value. Integers greater than 1 are plural, and lists with length greater than o...
Returns all CDS merged, used: - for TargQC general reports CDS coverage statistics for WGS - for Seq2C CNV calling when no capture BED available def get_merged_cds(genome): """ Returns all CDS merged, used: - for TargQC general reports CDS coverage statistics for WGS - for Seq2C CNV calling whe...
:param relative_path: relative path of the file inside the repository :param genome: genome name. Can contain chromosome name after comma, like hg19-chr20, in case of BED, the returning BedTool will be with added filter. :return: BedTools object if it's a BED file, or filepath def _get(relat...
Run the provided command, logging details and checking for errors. def run(cmd, output_fpath=None, input_fpath=None, checks=None, stdout_to_outputfile=True, stdout_tx=True, reuse=False, env_vars=None): """Run the provided command, logging details and checking for errors. """ if output_fpath and reu...
fixing java.lang.Double.parseDouble error on entries like "6,082.49" def _correct_qualimap_genome_results(samples): """ fixing java.lang.Double.parseDouble error on entries like "6,082.49" """ for s in samples: if verify_file(s.qualimap_genome_results_fpath): correction_is_needed = Fals...
replacing Qualimap insert size histogram with Picard one. def _correct_qualimap_insert_size_histogram(work_dir, samples): """ replacing Qualimap insert size histogram with Picard one. """ for s in samples: qualimap1_dirname = dirname(s.qualimap_ins_size_hist_fpath).replace('raw_data_qualimapReport'...
Normalize the length of a vector to one def norm_vec(vector): """Normalize the length of a vector to one""" assert len(vector) == 3 v = np.array(vector) return v/np.sqrt(np.sum(v**2))
Rotate all points of a list, such that `axis==[0,1,0]` This is accomplished by rotating in the x-z-plane by phi into the y-z-plane, then rotation in the y-z-plane by theta up to [0,1,0], and finally rotating back in the x-z-plane by -phi. Parameters ---------- points: list-like with elements o...
Compute rotation matrix to go from [0,0,1] to `point`. First, the matrix rotates to in the polar direction. Then, a rotation about the y-axis is performed to match the azimuthal angle in the x-z-plane. This rotation matrix is required for the correct 3D orientation of the backpropagated projection...
Compute rotation matrix to go from [0,0,1] to `point`, while taking into account the tilted axis of rotation. First, the matrix rotates to in the polar direction. Then, a rotation about the y-axis is performed to match the azimuthal angle in the x-z-plane. This rotation matrix is required for the ...
For a given tilt of the rotational axis `tilted_axis`, compute the points on a unit sphere that correspond to the distribution `angles` along the great circle about this axis. Parameters ---------- angles: 1d ndarray The angles that will be distributed on the great circle. tilted_axis: ...
r"""3D backpropagation with a tilted axis of rotation Three-dimensional diffraction tomography reconstruction algorithm for scattering of a plane wave :math:`u_0(\mathbf{r}) = u_0(x,y,z)` by a dielectric object with refractive index :math:`n(x,y,z)`. This method implements the 3D backpropagati...
Given a set of file names, produce a list of names consisting of the uniq parts of the names. This works from the end of the name. Chunks of the name are split on '.' and '-'. For example: A.foo.bar.txt B.foo.bar.txt returns: ['A','B'] AA.BB.foo.txt CC.foo....
Executes an process in the analysis with the given message. It also handles the start and stop signals in case a process_id is given. def run_process(self, analysis, action_name, message='__nomessagetoken__'): """Executes an process in the analysis with the given message. It also hand...
Check git to avoid overwriting user changes. def check_git_unchanged(filename, yes=False): """Check git to avoid overwriting user changes.""" if check_staged(filename): s = 'There are staged changes in {}, overwrite? [y/n] '.format(filename) if yes or input(s) in ('y', 'yes'): retur...
Check if there are 'changes to be committed' in the index. def check_staged(filename=None): """Check if there are 'changes to be committed' in the index.""" retcode, _, stdout = git['diff-index', '--quiet', '--cached', 'HEAD', filename].run(retcode=None) if retcode == 1: ...
Executes an action in the analysis with the given message. It also handles the start and stop signals in the case that message is a `dict` with a key ``__process_id``. :param str action_name: Name of the action to trigger. :param message: Message. :param callback: A...
Download `url` to `dest` def dl_file(url, dest, chunk_size=6553): """Download `url` to `dest`""" import urllib3 http = urllib3.PoolManager() r = http.request('GET', url, preload_content=False) with dest.open('wb') as out: while True: data = r.read(chunk_size) if data...
Extract an lzma file and return the temporary file name def extract_lzma(path): """Extract an lzma file and return the temporary file name""" tlfile = pathlib.Path(path) # open lzma file with tlfile.open("rb") as td: data = lzma.decompress(td.read()) # write temporary tar file fd, tmpna...
Return path of an example data file Return the full path to an example data file name. If the file does not exist in the `datapath` directory, tries to download it from the ODTbrain GitHub repository. def get_file(fname, datapath=datapath): """Return path of an example data file Return the full p...
Load example data def load_data(fname, kwargs): """Load example data""" fname = get_file(fname) if fname.suffix == ".lzma": return load_tar_lzma_data(fname) elif fname.suffix == ".zip": return load_zip_data(fname, kwargs)
Load example sinogram data from a .tar.lzma file def load_tar_lzma_data(tlfile): """Load example sinogram data from a .tar.lzma file""" tmpname = extract_lzma(tlfile) # open tar file fields_real = [] fields_imag = [] phantom = [] parms = {} with tarfile.open(tmpname, "r") as t: ...
Load example sinogram data from a .zip file def load_zip_data(zipname, f_sino_real, f_sino_imag, f_angles=None, f_phantom=None, f_info=None): """Load example sinogram data from a .zip file""" ret = [] with zipfile.ZipFile(str(zipname)) as arc: sino_real = np.loadtxt(arc.open(f_sin...
r"""2D Fourier mapping with the Fourier diffraction theorem Two-dimensional diffraction tomography reconstruction algorithm for scattering of a plane wave :math:`u_0(\mathbf{r}) = u_0(x,z)` by a dielectric object with refractive index :math:`n(x,z)`. This function implements the solution by in...
Decorator to create an output filename from an output filename with the specified extension. Changes the extension, in_file is transformed to a new type. Takes functions like this to decorate: f(in_file, out_dir=None, out_file=None) or, f(in_file=in_file, out_dir=None, out_file=None) examples:...
Decorator to create an output filename from an input filename by adding a word onto the stem. in_file is filtered by the function and the results are written to out_file. You would want to use this over transform_to if you don't know the extension of the file going in. This also memoizes the output file...
Context manager to temporarily change to a new directory. http://lucentbeing.com/blog/context-managers-and-the-with-statement-in-python/ def chdir(new_dir): """Context manager to temporarily change to a new directory. http://lucentbeing.com/blog/context-managers-and-the-with-statement-in-python/ """ ...
Check if a file exists, is non-empty and is more recent than cmp_fname. def file_uptodate(fname, cmp_fname): """Check if a file exists, is non-empty and is more recent than cmp_fname. """ try: return (file_exists(fname) and file_exists(cmp_fname) and getmtime(fname) >= getmtime(cmp_...
Overwrite a file in place with a short message to save disk. This keeps files as a sanity check on processes working, but saves disk by replacing them with a short message. def save_diskspace(fname, reason, config): """Overwrite a file in place with a short message to save disk. This keeps files as a...
Create relative symlinks and handle associated biological index files. def symlink_plus(orig, new): """Create relative symlinks and handle associated biological index files. """ for ext in ["", ".idx", ".gbi", ".tbi", ".bai"]: if os.path.exists(orig + ext) and not os.path.lexists(new + ext): ...
Use a predicate to partition entries into false entries and true entries def partition(pred, iterable): 'Use a predicate to partition entries into false entries and true entries' # partition(is_odd, range(10)) --> 0 2 4 6 8 and 1 3 5 7 9 t1, t2 = itertools.tee(iterable) try: return itertools...
look up if you can get a tuple of values from a nested dictionary, each item in the tuple a deeper layer example: get_in({1: {2: 3}}, (1, 2)) -> 3 example: get_in({1: {2: 3}}, (2, 3)) -> {} def get_in(d, t, default=None): """ look up if you can get a tuple of values from a nested dictionary, e...
returns the path to an executable or None if it can't be found def which(program): """ returns the path to an executable or None if it can't be found """ def is_exe(_fpath): return os.path.isfile(_fpath) and os.access(_fpath, os.X_OK) fpath, fname = os.path.split(program) if fpath: ...
Expand ~ and ~user constructs. If user or $HOME is unknown, do nothing. def expanduser(path): """Expand ~ and ~user constructs. If user or $HOME is unknown, do nothing.""" if path[:1] != '~': return path i, n = 1, len(path) while i < n and path[i] not in '/\\': i = i + 1 ...

Invoke the `UpdateItem`_ function. Edits an existing item's attributes, or adds a new item to the table if it does not already exist. You can put, delete, or add attribute values. You can also perform a conditional update on an existing item (insert a new attribute name-value pair if it...

A `Query`_ operation uses the primary key of a table or a secondary index to directly access items from that table or index. :param str table_name: The name of the table containing the requested items. :param bool consistent_read: Determines the read consistency model: If ...

The `Scan`_ operation returns one or more items and item attributes by accessing every item in a table or a secondary index. If the total number of scanned items exceeds the maximum data set size limit of 1 MB, the scan stops and results are returned to the user as a ``LastEvaluatedKey`...

Execute a DynamoDB action with the given parameters. The method will retry requests that failed due to OS level errors or when being throttled by DynamoDB. :param str action: DynamoDB action to invoke :param dict parameters: parameters to send into the action :rtype: tornado.con...

Assign a method to invoke when a request has encountered an unrecoverable error in an action execution. :param method callback: The method to invoke def set_error_callback(self, callback): """Assign a method to invoke when a request has encountered an unrecoverable error in an action e...

Assign a method to invoke when a request has completed gathering measurements. :param method callback: The method to invoke def set_instrumentation_callback(self, callback): """Assign a method to invoke when a request has completed gathering measurements. :param method callbac...

Invoke a DynamoDB action :param str action: DynamoDB action to invoke :param dict parameters: parameters to send into the action :param int attempt: Which attempt number this is :param list measurements: A list for accumulating request measurements :rtype: tornado.concurrent.Fut...

Invoked when the HTTP request to the DynamoDB has returned and is responsible for setting the future result or exception based upon the HTTP response provided. :param str action: The action that was taken :param str table: The table name the action was made against :param int at...

Process the raw AWS response, returning either the mapped exception or deserialized response. :param tornado.concurrent.Future response: The request future :rtype: dict or list :raises: sprockets_dynamodb.exceptions.DynamoDBException def _process_response(response): """Process...

Write and obj in bdb. :param obj: value to be written in bdb. :param resource_id: id to make possible read and search for an resource. :return: id of the transaction def write(self, obj, resource_id=None): """Write and obj in bdb. :param obj: value to be written in bdb. ...

Read and obj in bdb using the tx_id. :param resource_id: id of the transaction to be read. :return: value with the data, transaction id and transaction. def _get(self, tx_id): """Read and obj in bdb using the tx_id. :param resource_id: id of the transaction to be read. :return...

Update and obj in bdb using the tx_id. :param metadata: new metadata for the transaction. :param tx_id: id of the transaction to be updated. :return: id of the transaction. def _update(self, metadata, tx_id, resource_id): """Update and obj in bdb using the tx_id. :param metada...

List all the objects saved in the namespace. :param search_from: TBI :param search_to: TBI :param offset: TBI :param limit: max number of values to be shows. :return: list with transactions. def list(self, search_from=None, search_to=None, limit=None): """List all ...

List all the objects saved in the namespace. :param search_from: TBI :param search_to: TBI :param offset: TBI :param limit: max number of values to be shows. :return: list with transactions. def _list(self): """List all the objects saved in the namespace. :para...

Query to bdb namespace. :param query_string: query in string format. :return: list of transactions that match with the query. def query(self, search_model: QueryModel): """Query to bdb namespace. :param query_string: query in string format. :return: list of transactions that m...

Delete a transaction. Read documentation about CRAB model in https://blog.bigchaindb.com/crab-create-retrieve-append-burn-b9f6d111f460. :param tx_id: transaction id :return: def _delete(self, tx_id): """Delete a transaction. Read documentation about CRAB model in https://blog.bigchaindb.com/cr...

Return the tx_id of the first transaction. :param tx_id: Transaction id to start the recursive search. :return Transaction id parent. def get_asset_id(self, tx_id): """Return the tx_id of the first transaction. :param tx_id: Transaction id to start the recursive search. :retur...

write ENVI header files Parameters ---------- data: str or dict the file or dictionary to get the info from filename: str the HDR file to write Returns ------- def hdr(data, filename): """ write ENVI header files Parameters ---------- data: str or dict ...

read a HDR file into a dictionary http://gis.stackexchange.com/questions/48618/how-to-read-write-envi-metadata-using-gdal Returns ------- dict the hdr file metadata attributes def __hdr2dict(self): """ read a HDR file into a dictionary http://gis.stac...

write object to an ENVI header file def write(self, filename='same'): """ write object to an ENVI header file """ if filename == 'same': filename = self.filename if not filename.endswith('.hdr'): filename += '.hdr' with open(filename, 'w') as out:...

Setup of maximum speed def MaxSpeed(self, speed): ' Setup of maximum speed ' spi.SPI_write_byte(self.CS, 0x07) # Max Speed setup spi.SPI_write_byte(self.CS, 0x00) spi.SPI_write_byte(self.CS, speed)

Go to Zero position def GoZero(self, speed): ' Go to Zero position ' self.ReleaseSW() spi.SPI_write_byte(self.CS, 0x82 | (self.Dir & 1)) # Go to Zero spi.SPI_write_byte(self.CS, 0x00) spi.SPI_write_byte(self.CS, speed) while self.IsBusy(): pass ...

Move some distance units from current position def Move(self, units): ' Move some distance units from current position ' steps = units * self.SPU # translate units to steps if steps > 0: # look for direction spi.SPI_write_byte(self.CS, 0x40...

Report given status bit def ReadStatusBit(self, bit): ' Report given status bit ' spi.SPI_write_byte(self.CS, 0x39) # Read from address 0x19 (STATUS) spi.SPI_write_byte(self.CS, 0x00) data0 = spi.SPI_read_byte() # 1st byte spi.SPI_write_byte(self.CS, 0x00) da...

Writes a data to a SPI device selected by chipselect bit. def SPI_write_byte(self, chip_select, data): 'Writes a data to a SPI device selected by chipselect bit. ' self.bus.write_byte_data(self.address, chip_select, data)

Writes data to SPI device selected by chipselect bit. def SPI_write(self, chip_select, data): 'Writes data to SPI device selected by chipselect bit. ' dat = list(data) dat.insert(0, chip_select) return self.bus.write_i2c_block(self.address, dat);

Configure SPI interface parameters. def SPI_config(self,config): 'Configure SPI interface parameters.' self.bus.write_byte_data(self.address, 0xF0, config) return self.bus.read_byte_data(self.address, 0xF0)

Reads logic state on GPIO enabled slave-selects pins. def GPIO_read(self): 'Reads logic state on GPIO enabled slave-selects pins.' self.bus.write_byte_data(self.address, 0xF5, 0x0f) status = self.bus.read_byte(self.address) bits_values = dict([('SS0',status & 0x01 == 0x01),('SS1',status...

Enable or disable slave-select pins as gpio. def GPIO_config(self, gpio_enable, gpio_config): 'Enable or disable slave-select pins as gpio.' self.bus.write_byte_data(self.address, 0xF6, gpio_enable) self.bus.write_byte_data(self.address, 0xF7, gpio_config) return

Returns sensors I2C address. def get_address(self): """ Returns sensors I2C address. """ LOGGER.debug("Reading RPS01A sensor's address.",) return self.bus.read_byte_data(self.address, self.address_reg)

Returns programmed zero position in OTP memory. def get_zero_position(self): """ Returns programmed zero position in OTP memory. """ LSB = self.bus.read_byte_data(self.address, self.zero_position_MSB) MSB = self.bus.read_byte_data(self.address, self.zero_position_LSB) D...

Returns sensor's Automatic Gain Control actual value. 0 - Represents high magtetic field 0xFF - Represents low magnetic field def get_agc_value(self): """ Returns sensor's Automatic Gain Control actual value. 0 - Represents high magtetic field 0xFF...

Reads diagnostic data from the sensor. OCF (Offset Compensation Finished) - logic high indicates the finished Offset Compensation Algorithm. After power up the flag remains always to logic high. COF (Cordic Overflow) - logic high indicates an out of range error in the CORDIC part. When this bit is set,...

Retuns measured angle in degrees in range 0-360. def get_angle(self, verify = False): """ Retuns measured angle in degrees in range 0-360. """ LSB = self.bus.read_byte_data(self.address, self.angle_LSB) MSB = self.bus.read_byte_data(self.address, self.angle_MSB) DATA = (...

Annotating BED file based on reference features annotations. def main(input_bed, output_file, output_features=False, genome=None, only_canonical=False, short=False, extended=False, high_confidence=False, ambiguities_method=False, coding_only=False, collapse_exons=False, work_dir=False, is_debug=False...

% of Full Charge def StateOfCharge(self): """ % of Full Charge """ return (self.bus.read_byte_data(self.address, 0x02) + self.bus.read_byte_data(self.address, 0x03) * 256)

Get cells chemistry def Chemistry(self): ''' Get cells chemistry ''' length = self.bus.read_byte_data(self.address, 0x79) chem = [] for n in range(length): chem.append(self.bus.read_byte_data(self.address, 0x7A + n)) return chem

r"""(slow) 2D reconstruction with the Fourier diffraction theorem Two-dimensional diffraction tomography reconstruction algorithm for scattering of a plane wave :math:`u_0(\mathbf{r}) = u_0(x,z)` by a dielectric object with refractive index :math:`n(x,z)`. This function implements the solution...

r"""2D backpropagation with the Fourier diffraction theorem Two-dimensional diffraction tomography reconstruction algorithm for scattering of a plane wave :math:`u_0(\mathbf{r}) = u_0(x,z)` by a dielectric object with refractive index :math:`n(x,z)`. This method implements the 2D backpropagati...

triangles. Colors: - http://paletton.com/#uid=70l150klllletuehUpNoMgTsdcs shade 2 def color(x, y): """triangles. Colors: - http://paletton.com/#uid=70l150klllletuehUpNoMgTsdcs shade 2 """ if (x-4) > (y-4) and -(y-4) <= (x-4): # right return "#CDB95B" elif (x-4) > (y-4...

Reads data from desired register only once. def single_read(self, register): ''' Reads data from desired register only once. ''' comm_reg = (0b00010 << 3) + register if register == self.AD7730_STATUS_REG: bytes_num = 1 elif register == self.AD7730_...

RDY - Ready Bit. This bit provides the status of the RDY flag from the part. The status and function of this bit is the same as the RDY output pin. A number of events set the RDY bit high as indicated in Table XVIII in datasheet STDY - Steady Bit. This bit is updated when the filter writes a result to the Data...

def setMode(self ,mode = self.AD7730_IDLE_MODE ,polarity = self.AD7730_UNIPOLAR_MODE ,den = self.AD7730_IODISABLE_MODE ,iovalue = 0b00 ,data_lenght = self.AD7730_24bitDATA_MODE ,reference = self.AD77...

get N random headers from a fastq file without reading the whole thing into memory modified from: http://www.biostars.org/p/6544/ def downsample(work_dir, sample_name, fastq_left_fpath, fastq_right_fpath, downsample_to, num_pairs=None): """ get N random headers from a fastq file without reading the who...

The physical value RH given above corresponds to the relative humidity above liquid water according to World Meteorological Organization (WMO) def get_hum(self, raw = False): """ The physical value RH given above corresponds to the relative humidity above liquid water according ...

4.12 Checksum Calculation from an unsigned short input def _calculate_checksum(value): """4.12 Checksum Calculation from an unsigned short input""" # CRC polynomial = 0x131 # //P(x)=x^8+x^5+x^4+1 = 100110001 crc = 0xFF # calculates 8-Bit checksum with given polynomial ...

Run when button is pressed. def run(self): """Run when button is pressed.""" inside = 0 for draws in range(1, self.data['samples']): # generate points and check whether they are inside the unit circle r1, r2 = (random(), random()) if r1 ** 2 + r2 ** 2 < 1.0:...

Decorator for action handlers. The action name is inferred from the function name. This also decorates the method with `tornado.gen.coroutine` so that `~tornado.concurrent.Future` can be yielded. def on(f): """Decorator for action handlers. The action name is inferred from the function name. ...

Decorator for action handlers. :param str action: explicit action name This also decorates the method with `tornado.gen.coroutine` so that `~tornado.concurrent.Future` can be yielded. def on_action(action): """Decorator for action handlers. :param str action: explicit action name This also ...

Initialize datastores for this analysis instance. This creates instances of :class:`.Datastore` at ``data`` and ``class_data`` with the datastore domains being the current id and the class name of this analysis respectively. Overwrite this method to use other datastore backends. def i...

Emit a signal to the frontend. :param str signal: name of the signal :param message: message to send :returns: return value from frontend emit function :rtype: tornado.concurrent.Future def emit(self, signal, message='__nomessagetoken__'): """Emit a signal to the frontend. ...

Set value at position i and return a Future. :rtype: tornado.concurrent.Future def set(self, i, value): """Set value at position i and return a Future. :rtype: tornado.concurrent.Future """ value_encoded = encode(value, self.get_change_trigger(i)) if i in self.data an...

Set a value at key and return a Future. :rtype: tornado.concurrent.Future def set(self, key, value): """Set a value at key and return a Future. :rtype: tornado.concurrent.Future """ value_encoded = encode(value, self.get_change_trigger(key)) if key in self.data and se...

Update. def update(self, new_data): """Update.""" for k, v in new_data.items(): self[k] = v return self

Trigger all callbacks that were set with on_change(). def trigger_all_change_callbacks(self): """Trigger all callbacks that were set with on_change().""" return [ ret for key in DatastoreLegacy.store[self.domain].keys() for ret in self.trigger_change_callbacks(key) ...

Set value at key and return a Future :rtype: tornado.concurrent.Future def set(self, key, value): """Set value at key and return a Future :rtype: tornado.concurrent.Future """ return DatastoreLegacy.store[self.domain].set(key, value)

Initialize datastore. Only sets values for keys that are not in the datastore already. :param dict key_value_pairs: A set of key value pairs to use to initialize the datastore. def init(self, key_value_pairs): """Initialize datastore. Only sets values for keys that are no...

Close and delete instance. def close(self): """Close and delete instance.""" # remove callbacks DatastoreLegacy.datastores[self.domain].remove(self) # delete data after the last instance is gone if self.release_storage and \ not DatastoreLegacy.datastores[self.domai...

Recursively add the current index (with respect to a repeated section) in all data dictionaries. def AddIndex(node, index=None): """ Recursively add the current index (with respect to a repeated section) in all data dictionaries. """ if isinstance(node, list): for i, item in enumerate(node): AddI...

Renerate documentation when it changes. def watch(): """Renerate documentation when it changes.""" # Start with a clean build sphinx_build['-b', 'html', '-E', 'docs', 'docs/_build/html'] & FG handler = ShellCommandTrick( shell_command='sphinx-build -b html docs docs/_build/html', patt...

Generate html and dirhtml output. def gen(skipdirhtml=False): """Generate html and dirhtml output.""" docs_changelog = 'docs/changelog.rst' check_git_unchanged(docs_changelog) pandoc('--from=markdown', '--to=rst', '--output=' + docs_changelog, 'CHANGELOG.md') if not skipdirhtml: sphinx_buil...

redraw the cross-hair on the horizontal slice plot Parameters ---------- x: int the x image coordinate y: int the y image coordinate Returns ------- def __reset_crosshair(self): """ redraw the cross-hair on the horizontal slice p...

set up the vertical profile plot Returns ------- def __init_vertical_plot(self): """ set up the vertical profile plot Returns ------- """ # clear the plot if lines have already been drawn on it if len(self.ax2.lines) > 0: self.ax2.cl...

respond to mouse clicks in the plot. This function responds to clicks on the first (horizontal slice) plot and updates the vertical profile and slice plots Parameters ---------- event: matplotlib.backend_bases.MouseEvent the click event object containing image coordi...

Returns a *function* suitable for passing as the more_formatters argument to Template. NOTE: In Java, this would be implemented using the 'Composite' pattern. A *list* of formatter lookup function behaves the same as a *single* formatter lookup funcion. Note the distinction between formatter *lookup* funct...

Use Python % format strings as template format specifiers. def PythonPercentFormat(format_str): """Use Python % format strings as template format specifiers.""" if format_str.startswith('printf '): fmt = format_str[len('printf '):] return lambda value: fmt % value else: return None

Returns whether the value should be considered a plural value. Integers greater than 1 are plural, and lists with length greater than one are too. def Plural(format_str): """Returns whether the value should be considered a plural value. Integers greater than 1 are plural, and lists with length greater than o...

Returns all CDS merged, used: - for TargQC general reports CDS coverage statistics for WGS - for Seq2C CNV calling when no capture BED available def get_merged_cds(genome): """ Returns all CDS merged, used: - for TargQC general reports CDS coverage statistics for WGS - for Seq2C CNV calling whe...

:param relative_path: relative path of the file inside the repository :param genome: genome name. Can contain chromosome name after comma, like hg19-chr20, in case of BED, the returning BedTool will be with added filter. :return: BedTools object if it's a BED file, or filepath def _get(relat...

Run the provided command, logging details and checking for errors. def run(cmd, output_fpath=None, input_fpath=None, checks=None, stdout_to_outputfile=True, stdout_tx=True, reuse=False, env_vars=None): """Run the provided command, logging details and checking for errors. """ if output_fpath and reu...

fixing java.lang.Double.parseDouble error on entries like "6,082.49" def _correct_qualimap_genome_results(samples): """ fixing java.lang.Double.parseDouble error on entries like "6,082.49" """ for s in samples: if verify_file(s.qualimap_genome_results_fpath): correction_is_needed = Fals...

replacing Qualimap insert size histogram with Picard one. def _correct_qualimap_insert_size_histogram(work_dir, samples): """ replacing Qualimap insert size histogram with Picard one. """ for s in samples: qualimap1_dirname = dirname(s.qualimap_ins_size_hist_fpath).replace('raw_data_qualimapReport'...

Normalize the length of a vector to one def norm_vec(vector): """Normalize the length of a vector to one""" assert len(vector) == 3 v = np.array(vector) return v/np.sqrt(np.sum(v**2))

Rotate all points of a list, such that `axis==[0,1,0]` This is accomplished by rotating in the x-z-plane by phi into the y-z-plane, then rotation in the y-z-plane by theta up to [0,1,0], and finally rotating back in the x-z-plane by -phi. Parameters ---------- points: list-like with elements o...

Compute rotation matrix to go from [0,0,1] to `point`. First, the matrix rotates to in the polar direction. Then, a rotation about the y-axis is performed to match the azimuthal angle in the x-z-plane. This rotation matrix is required for the correct 3D orientation of the backpropagated projection...

Compute rotation matrix to go from [0,0,1] to `point`, while taking into account the tilted axis of rotation. First, the matrix rotates to in the polar direction. Then, a rotation about the y-axis is performed to match the azimuthal angle in the x-z-plane. This rotation matrix is required for the ...

For a given tilt of the rotational axis `tilted_axis`, compute the points on a unit sphere that correspond to the distribution `angles` along the great circle about this axis. Parameters ---------- angles: 1d ndarray The angles that will be distributed on the great circle. tilted_axis: ...

r"""3D backpropagation with a tilted axis of rotation Three-dimensional diffraction tomography reconstruction algorithm for scattering of a plane wave :math:`u_0(\mathbf{r}) = u_0(x,y,z)` by a dielectric object with refractive index :math:`n(x,y,z)`. This method implements the 3D backpropagati...

Given a set of file names, produce a list of names consisting of the uniq parts of the names. This works from the end of the name. Chunks of the name are split on '.' and '-'. For example: A.foo.bar.txt B.foo.bar.txt returns: ['A','B'] AA.BB.foo.txt CC.foo....

Executes an process in the analysis with the given message. It also handles the start and stop signals in case a process_id is given. def run_process(self, analysis, action_name, message='__nomessagetoken__'): """Executes an process in the analysis with the given message. It also hand...

Check git to avoid overwriting user changes. def check_git_unchanged(filename, yes=False): """Check git to avoid overwriting user changes.""" if check_staged(filename): s = 'There are staged changes in {}, overwrite? [y/n] '.format(filename) if yes or input(s) in ('y', 'yes'): retur...

Check if there are 'changes to be committed' in the index. def check_staged(filename=None): """Check if there are 'changes to be committed' in the index.""" retcode, _, stdout = git['diff-index', '--quiet', '--cached', 'HEAD', filename].run(retcode=None) if retcode == 1: ...

Executes an action in the analysis with the given message. It also handles the start and stop signals in the case that message is a `dict` with a key ``__process_id``. :param str action_name: Name of the action to trigger. :param message: Message. :param callback: A...

Download `url` to `dest` def dl_file(url, dest, chunk_size=6553): """Download `url` to `dest`""" import urllib3 http = urllib3.PoolManager() r = http.request('GET', url, preload_content=False) with dest.open('wb') as out: while True: data = r.read(chunk_size) if data...

Extract an lzma file and return the temporary file name def extract_lzma(path): """Extract an lzma file and return the temporary file name""" tlfile = pathlib.Path(path) # open lzma file with tlfile.open("rb") as td: data = lzma.decompress(td.read()) # write temporary tar file fd, tmpna...

Return path of an example data file Return the full path to an example data file name. If the file does not exist in the `datapath` directory, tries to download it from the ODTbrain GitHub repository. def get_file(fname, datapath=datapath): """Return path of an example data file Return the full p...

Load example data def load_data(fname, **kwargs): """Load example data""" fname = get_file(fname) if fname.suffix == ".lzma": return load_tar_lzma_data(fname) elif fname.suffix == ".zip": return load_zip_data(fname, **kwargs)

Load example sinogram data from a .tar.lzma file def load_tar_lzma_data(tlfile): """Load example sinogram data from a .tar.lzma file""" tmpname = extract_lzma(tlfile) # open tar file fields_real = [] fields_imag = [] phantom = [] parms = {} with tarfile.open(tmpname, "r") as t: ...

Load example sinogram data from a .zip file def load_zip_data(zipname, f_sino_real, f_sino_imag, f_angles=None, f_phantom=None, f_info=None): """Load example sinogram data from a .zip file""" ret = [] with zipfile.ZipFile(str(zipname)) as arc: sino_real = np.loadtxt(arc.open(f_sin...

r"""2D Fourier mapping with the Fourier diffraction theorem Two-dimensional diffraction tomography reconstruction algorithm for scattering of a plane wave :math:`u_0(\mathbf{r}) = u_0(x,z)` by a dielectric object with refractive index :math:`n(x,z)`. This function implements the solution by in...

Decorator to create an output filename from an output filename with the specified extension. Changes the extension, in_file is transformed to a new type. Takes functions like this to decorate: f(in_file, out_dir=None, out_file=None) or, f(in_file=in_file, out_dir=None, out_file=None) examples:...

Decorator to create an output filename from an input filename by adding a word onto the stem. in_file is filtered by the function and the results are written to out_file. You would want to use this over transform_to if you don't know the extension of the file going in. This also memoizes the output file...

Context manager to temporarily change to a new directory. http://lucentbeing.com/blog/context-managers-and-the-with-statement-in-python/ def chdir(new_dir): """Context manager to temporarily change to a new directory. http://lucentbeing.com/blog/context-managers-and-the-with-statement-in-python/ """ ...

Check if a file exists, is non-empty and is more recent than cmp_fname. def file_uptodate(fname, cmp_fname): """Check if a file exists, is non-empty and is more recent than cmp_fname. """ try: return (file_exists(fname) and file_exists(cmp_fname) and getmtime(fname) >= getmtime(cmp_...

Overwrite a file in place with a short message to save disk. This keeps files as a sanity check on processes working, but saves disk by replacing them with a short message. def save_diskspace(fname, reason, config): """Overwrite a file in place with a short message to save disk. This keeps files as a...

Create relative symlinks and handle associated biological index files. def symlink_plus(orig, new): """Create relative symlinks and handle associated biological index files. """ for ext in ["", ".idx", ".gbi", ".tbi", ".bai"]: if os.path.exists(orig + ext) and not os.path.lexists(new + ext): ...

Use a predicate to partition entries into false entries and true entries def partition(pred, iterable): 'Use a predicate to partition entries into false entries and true entries' # partition(is_odd, range(10)) --> 0 2 4 6 8 and 1 3 5 7 9 t1, t2 = itertools.tee(iterable) try: return itertools...

look up if you can get a tuple of values from a nested dictionary, each item in the tuple a deeper layer example: get_in({1: {2: 3}}, (1, 2)) -> 3 example: get_in({1: {2: 3}}, (2, 3)) -> {} def get_in(d, t, default=None): """ look up if you can get a tuple of values from a nested dictionary, e...

returns the path to an executable or None if it can't be found def which(program): """ returns the path to an executable or None if it can't be found """ def is_exe(_fpath): return os.path.isfile(_fpath) and os.access(_fpath, os.X_OK) fpath, fname = os.path.split(program) if fpath: ...

Expand ~ and ~user constructs. If user or $HOME is unknown, do nothing. def expanduser(path): """Expand ~ and ~user constructs. If user or $HOME is unknown, do nothing.""" if path[:1] != '~': return path i, n = 1, len(path) while i < n and path[i] not in '/\\': i = i + 1 ...