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pyhys/minimalmodbus | minimalmodbus.py | _createBitpattern | def _createBitpattern(functioncode, value):
"""Create the bit pattern that is used for writing single bits.
This is basically a storage of numerical constants.
Args:
* functioncode (int): can be 5 or 15
* value (int): can be 0 or 1
Returns:
The bit pattern (string).
Raise... | python | def _createBitpattern(functioncode, value):
"""Create the bit pattern that is used for writing single bits.
This is basically a storage of numerical constants.
Args:
* functioncode (int): can be 5 or 15
* value (int): can be 0 or 1
Returns:
The bit pattern (string).
Raise... | [
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pyhys/minimalmodbus | minimalmodbus.py | _twosComplement | def _twosComplement(x, bits=16):
"""Calculate the two's complement of an integer.
Then also negative values can be represented by an upper range of positive values.
See https://en.wikipedia.org/wiki/Two%27s_complement
Args:
* x (int): input integer.
* bits (int): number of bits, must b... | python | def _twosComplement(x, bits=16):
"""Calculate the two's complement of an integer.
Then also negative values can be represented by an upper range of positive values.
See https://en.wikipedia.org/wiki/Two%27s_complement
Args:
* x (int): input integer.
* bits (int): number of bits, must b... | [
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pyhys/minimalmodbus | minimalmodbus.py | _setBitOn | def _setBitOn(x, bitNum):
"""Set bit 'bitNum' to True.
Args:
* x (int): The value before.
* bitNum (int): The bit number that should be set to True.
Returns:
The value after setting the bit. This is an integer.
For example:
For x = 4 (dec) = 0100 (bin), setting bit num... | python | def _setBitOn(x, bitNum):
"""Set bit 'bitNum' to True.
Args:
* x (int): The value before.
* bitNum (int): The bit number that should be set to True.
Returns:
The value after setting the bit. This is an integer.
For example:
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pyhys/minimalmodbus | minimalmodbus.py | _calculateCrcString | def _calculateCrcString(inputstring):
"""Calculate CRC-16 for Modbus.
Args:
inputstring (str): An arbitrary-length message (without the CRC).
Returns:
A two-byte CRC string, where the least significant byte is first.
"""
_checkString(inputstring, description='input CRC string')
... | python | def _calculateCrcString(inputstring):
"""Calculate CRC-16 for Modbus.
Args:
inputstring (str): An arbitrary-length message (without the CRC).
Returns:
A two-byte CRC string, where the least significant byte is first.
"""
_checkString(inputstring, description='input CRC string')
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pyhys/minimalmodbus | minimalmodbus.py | _calculateLrcString | def _calculateLrcString(inputstring):
"""Calculate LRC for Modbus.
Args:
inputstring (str): An arbitrary-length message (without the beginning
colon and terminating CRLF). It should already be decoded from hex-string.
Returns:
A one-byte LRC bytestring (not encoded to hex-string)
... | python | def _calculateLrcString(inputstring):
"""Calculate LRC for Modbus.
Args:
inputstring (str): An arbitrary-length message (without the beginning
colon and terminating CRLF). It should already be decoded from hex-string.
Returns:
A one-byte LRC bytestring (not encoded to hex-string)
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pyhys/minimalmodbus | minimalmodbus.py | _checkMode | def _checkMode(mode):
"""Check that the Modbus mode is valie.
Args:
mode (string): The Modbus mode (MODE_RTU or MODE_ASCII)
Raises:
TypeError, ValueError
"""
if not isinstance(mode, str):
raise TypeError('The {0} should be a string. Given: {1!r}'.format("mode", mode))
... | python | def _checkMode(mode):
"""Check that the Modbus mode is valie.
Args:
mode (string): The Modbus mode (MODE_RTU or MODE_ASCII)
Raises:
TypeError, ValueError
"""
if not isinstance(mode, str):
raise TypeError('The {0} should be a string. Given: {1!r}'.format("mode", mode))
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pyhys/minimalmodbus | minimalmodbus.py | _checkFunctioncode | def _checkFunctioncode(functioncode, listOfAllowedValues=[]):
"""Check that the given functioncode is in the listOfAllowedValues.
Also verifies that 1 <= function code <= 127.
Args:
* functioncode (int): The function code
* listOfAllowedValues (list of int): Allowed values. Use *None* to b... | python | def _checkFunctioncode(functioncode, listOfAllowedValues=[]):
"""Check that the given functioncode is in the listOfAllowedValues.
Also verifies that 1 <= function code <= 127.
Args:
* functioncode (int): The function code
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pyhys/minimalmodbus | minimalmodbus.py | _checkResponseByteCount | def _checkResponseByteCount(payload):
"""Check that the number of bytes as given in the response is correct.
The first byte in the payload indicates the length of the payload (first byte not counted).
Args:
payload (string): The payload
Raises:
TypeError, ValueError
"""
POSIT... | python | def _checkResponseByteCount(payload):
"""Check that the number of bytes as given in the response is correct.
The first byte in the payload indicates the length of the payload (first byte not counted).
Args:
payload (string): The payload
Raises:
TypeError, ValueError
"""
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pyhys/minimalmodbus | minimalmodbus.py | _checkResponseRegisterAddress | def _checkResponseRegisterAddress(payload, registeraddress):
"""Check that the start adress as given in the response is correct.
The first two bytes in the payload holds the address value.
Args:
* payload (string): The payload
* registeraddress (int): The register address (use decimal numb... | python | def _checkResponseRegisterAddress(payload, registeraddress):
"""Check that the start adress as given in the response is correct.
The first two bytes in the payload holds the address value.
Args:
* payload (string): The payload
* registeraddress (int): The register address (use decimal numb... | [
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pyhys/minimalmodbus | minimalmodbus.py | _checkResponseNumberOfRegisters | def _checkResponseNumberOfRegisters(payload, numberOfRegisters):
"""Check that the number of written registers as given in the response is correct.
The bytes 2 and 3 (zero based counting) in the payload holds the value.
Args:
* payload (string): The payload
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"""Check that the number of written registers as given in the response is correct.
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Args:
* payload (string): The payload
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pyhys/minimalmodbus | minimalmodbus.py | _checkResponseWriteData | def _checkResponseWriteData(payload, writedata):
"""Check that the write data as given in the response is correct.
The bytes 2 and 3 (zero based counting) in the payload holds the write data.
Args:
* payload (string): The payload
* writedata (string): The data to write, length should be 2 ... | python | def _checkResponseWriteData(payload, writedata):
"""Check that the write data as given in the response is correct.
The bytes 2 and 3 (zero based counting) in the payload holds the write data.
Args:
* payload (string): The payload
* writedata (string): The data to write, length should be 2 ... | [
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pyhys/minimalmodbus | minimalmodbus.py | _checkString | def _checkString(inputstring, description, minlength=0, maxlength=None):
"""Check that the given string is valid.
Args:
* inputstring (string): The string to be checked
* description (string): Used in error messages for the checked inputstring
* minlength (int): Minimum length of the st... | python | def _checkString(inputstring, description, minlength=0, maxlength=None):
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Args:
* inputstring (string): The string to be checked
* description (string): Used in error messages for the checked inputstring
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pyhys/minimalmodbus | minimalmodbus.py | _checkInt | def _checkInt(inputvalue, minvalue=None, maxvalue=None, description='inputvalue'):
"""Check that the given integer is valid.
Args:
* inputvalue (int or long): The integer to be checked
* minvalue (int or long, or None): Minimum value of the integer
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* inputvalue (int or long): The integer to be checked
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pyhys/minimalmodbus | minimalmodbus.py | _checkNumerical | def _checkNumerical(inputvalue, minvalue=None, maxvalue=None, description='inputvalue'):
"""Check that the given numerical value is valid.
Args:
* inputvalue (numerical): The value to be checked.
* minvalue (numerical): Minimum value Use None to skip this part of the test.
* maxvalue (... | python | def _checkNumerical(inputvalue, minvalue=None, maxvalue=None, description='inputvalue'):
"""Check that the given numerical value is valid.
Args:
* inputvalue (numerical): The value to be checked.
* minvalue (numerical): Minimum value Use None to skip this part of the test.
* maxvalue (... | [
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pyhys/minimalmodbus | minimalmodbus.py | _checkBool | def _checkBool(inputvalue, description='inputvalue'):
"""Check that the given inputvalue is a boolean.
Args:
* inputvalue (boolean): The value to be checked.
* description (string): Used in error messages for the checked inputvalue.
Raises:
TypeError, ValueError
"""
_check... | python | def _checkBool(inputvalue, description='inputvalue'):
"""Check that the given inputvalue is a boolean.
Args:
* inputvalue (boolean): The value to be checked.
* description (string): Used in error messages for the checked inputvalue.
Raises:
TypeError, ValueError
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pyhys/minimalmodbus | minimalmodbus.py | _getDiagnosticString | def _getDiagnosticString():
"""Generate a diagnostic string, showing the module version, the platform, current directory etc.
Returns:
A descriptive string.
"""
text = '\n## Diagnostic output from minimalmodbus ## \n\n'
text += 'Minimalmodbus version: ' + __version__ + '\n'
text += 'Mi... | python | def _getDiagnosticString():
"""Generate a diagnostic string, showing the module version, the platform, current directory etc.
Returns:
A descriptive string.
"""
text = '\n## Diagnostic output from minimalmodbus ## \n\n'
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text += 'Mi... | [
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.read_bit | def read_bit(self, registeraddress, functioncode=2):
"""Read one bit from the slave.
Args:
* registeraddress (int): The slave register address (use decimal numbers, not hex).
* functioncode (int): Modbus function code. Can be 1 or 2.
Returns:
The bit value 0... | python | def read_bit(self, registeraddress, functioncode=2):
"""Read one bit from the slave.
Args:
* registeraddress (int): The slave register address (use decimal numbers, not hex).
* functioncode (int): Modbus function code. Can be 1 or 2.
Returns:
The bit value 0... | [
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.write_bit | def write_bit(self, registeraddress, value, functioncode=5):
"""Write one bit to the slave.
Args:
* registeraddress (int): The slave register address (use decimal numbers, not hex).
* value (int): 0 or 1
* functioncode (int): Modbus function code. Can be 5 or 15.
... | python | def write_bit(self, registeraddress, value, functioncode=5):
"""Write one bit to the slave.
Args:
* registeraddress (int): The slave register address (use decimal numbers, not hex).
* value (int): 0 or 1
* functioncode (int): Modbus function code. Can be 5 or 15.
... | [
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.read_register | def read_register(self, registeraddress, numberOfDecimals=0, functioncode=3, signed=False):
"""Read an integer from one 16-bit register in the slave, possibly scaling it.
The slave register can hold integer values in the range 0 to 65535 ("Unsigned INT16").
Args:
* registeraddress ... | python | def read_register(self, registeraddress, numberOfDecimals=0, functioncode=3, signed=False):
"""Read an integer from one 16-bit register in the slave, possibly scaling it.
The slave register can hold integer values in the range 0 to 65535 ("Unsigned INT16").
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.write_register | def write_register(self, registeraddress, value, numberOfDecimals=0, functioncode=16, signed=False):
"""Write an integer to one 16-bit register in the slave, possibly scaling it.
The slave register can hold integer values in the range 0 to 65535 ("Unsigned INT16").
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"""Write an integer to one 16-bit register in the slave, possibly scaling it.
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.read_float | def read_float(self, registeraddress, functioncode=3, numberOfRegisters=2):
"""Read a floating point number from the slave.
Floats are stored in two or more consecutive 16-bit registers in the slave. The
encoding is according to the standard IEEE 754.
There are differences in the byte ... | python | def read_float(self, registeraddress, functioncode=3, numberOfRegisters=2):
"""Read a floating point number from the slave.
Floats are stored in two or more consecutive 16-bit registers in the slave. The
encoding is according to the standard IEEE 754.
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.write_float | def write_float(self, registeraddress, value, numberOfRegisters=2):
"""Write a floating point number to the slave.
Floats are stored in two or more consecutive 16-bit registers in the slave.
Uses Modbus function code 16.
For discussion on precision, number of registers and on byte ord... | python | def write_float(self, registeraddress, value, numberOfRegisters=2):
"""Write a floating point number to the slave.
Floats are stored in two or more consecutive 16-bit registers in the slave.
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.read_string | def read_string(self, registeraddress, numberOfRegisters=16, functioncode=3):
"""Read a string from the slave.
Each 16-bit register in the slave are interpreted as two characters (1 byte = 8 bits).
For example 16 consecutive registers can hold 32 characters (32 bytes).
Args:
... | python | def read_string(self, registeraddress, numberOfRegisters=16, functioncode=3):
"""Read a string from the slave.
Each 16-bit register in the slave are interpreted as two characters (1 byte = 8 bits).
For example 16 consecutive registers can hold 32 characters (32 bytes).
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... | [
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.write_string | def write_string(self, registeraddress, textstring, numberOfRegisters=16):
"""Write a string to the slave.
Each 16-bit register in the slave are interpreted as two characters (1 byte = 8 bits).
For example 16 consecutive registers can hold 32 characters (32 bytes).
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"""Write a string to the slave.
Each 16-bit register in the slave are interpreted as two characters (1 byte = 8 bits).
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pyhys/minimalmodbus | minimalmodbus.py | Instrument.write_registers | def write_registers(self, registeraddress, values):
"""Write integers to 16-bit registers in the slave.
The slave register can hold integer values in the range 0 to 65535 ("Unsigned INT16").
Uses Modbus function code 16.
The number of registers that will be written is defined by the l... | python | def write_registers(self, registeraddress, values):
"""Write integers to 16-bit registers in the slave.
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pyhys/minimalmodbus | minimalmodbus.py | Instrument._communicate | def _communicate(self, request, number_of_bytes_to_read):
"""Talk to the slave via a serial port.
Args:
request (str): The raw request that is to be sent to the slave.
number_of_bytes_to_read (int): number of bytes to read
Returns:
The raw data (string) retu... | python | def _communicate(self, request, number_of_bytes_to_read):
"""Talk to the slave via a serial port.
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request (str): The raw request that is to be sent to the slave.
number_of_bytes_to_read (int): number of bytes to read
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TaylorSMarks/playsound | playsound.py | _playsoundWin | def _playsoundWin(sound, block = True):
'''
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Probably works on Windows XP thru Windows 10. Probably works with all
versions of Python.
Inspired by (but not copie... | python | def _playsoundWin(sound, block = True):
'''
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Probably works on Windows XP thru Windows 10. Probably works with all
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TaylorSMarks/playsound | playsound.py | _playsoundOSX | def _playsoundOSX(sound, block = True):
'''
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Probably works on OS X 10.5 and newer. Probably works with all versions of
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'''
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TaylorSMarks/playsound | playsound.py | _playsoundNix | def _playsoundNix(sound, block=True):
"""Play a sound using GStreamer.
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"""
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"""
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mfitzp/padua | padua/filters.py | remove_rows_matching | def remove_rows_matching(df, column, match):
"""
Return a ``DataFrame`` with rows where `column` values match `match` are removed.
The selected `column` series of values from the supplied Pandas ``DataFrame`` is compared
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"""
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mfitzp/padua | padua/filters.py | remove_rows_containing | def remove_rows_containing(df, column, match):
"""
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"""
Return a ``DataFrame`` with rows where `column` values containing `match` are removed.
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mfitzp/padua | padua/filters.py | filter_localization_probability | def filter_localization_probability(df, threshold=0.75):
"""
Remove rows with a localization probability below 0.75
Return a ``DataFrame`` where the rows with a value < `threshold` (default 0.75) in column 'Localization prob' are removed.
Filters data to remove poorly localized peptides (non Class-I by... | python | def filter_localization_probability(df, threshold=0.75):
"""
Remove rows with a localization probability below 0.75
Return a ``DataFrame`` where the rows with a value < `threshold` (default 0.75) in column 'Localization prob' are removed.
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mfitzp/padua | padua/filters.py | minimum_valid_values_in_any_group | def minimum_valid_values_in_any_group(df, levels=None, n=1, invalid=np.nan):
"""
Filter ``DataFrame`` by at least n valid values in at least one group.
Taking a Pandas ``DataFrame`` with a ``MultiIndex`` column index, filters rows to remove
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"""
Filter ``DataFrame`` by at least n valid values in at least one group.
Taking a Pandas ``DataFrame`` with a ``MultiIndex`` column index, filters rows to remove
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mfitzp/padua | padua/filters.py | search | def search(df, match, columns=['Proteins','Protein names','Gene names']):
"""
Search for a given string in a set of columns in a processed ``DataFrame``.
Returns a filtered ``DataFrame`` where `match` is contained in one of the `columns`.
:param df: Pandas ``DataFrame``
:param match: ``str`` to se... | python | def search(df, match, columns=['Proteins','Protein names','Gene names']):
"""
Search for a given string in a set of columns in a processed ``DataFrame``.
Returns a filtered ``DataFrame`` where `match` is contained in one of the `columns`.
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mfitzp/padua | padua/filters.py | filter_select_columns_intensity | def filter_select_columns_intensity(df, prefix, columns):
"""
Filter dataframe to include specified columns, retaining any Intensity columns.
"""
# Note: I use %s.+ (not %s.*) so it forces a match with the prefix string, ONLY if it is followed by something.
return df.filter(regex='^(%s.+|%s)$' % (pr... | python | def filter_select_columns_intensity(df, prefix, columns):
"""
Filter dataframe to include specified columns, retaining any Intensity columns.
"""
# Note: I use %s.+ (not %s.*) so it forces a match with the prefix string, ONLY if it is followed by something.
return df.filter(regex='^(%s.+|%s)$' % (pr... | [
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mfitzp/padua | padua/filters.py | filter_intensity | def filter_intensity(df, label="", with_multiplicity=False):
"""
Filter to include only the Intensity values with optional specified label, excluding other
Intensity measurements, but retaining all other columns.
"""
label += ".*__\d" if with_multiplicity else ""
dft = df.filter(regex="^(?!Int... | python | def filter_intensity(df, label="", with_multiplicity=False):
"""
Filter to include only the Intensity values with optional specified label, excluding other
Intensity measurements, but retaining all other columns.
"""
label += ".*__\d" if with_multiplicity else ""
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mfitzp/padua | padua/filters.py | filter_ratio | def filter_ratio(df, label="", with_multiplicity=False):
"""
Filter to include only the Ratio values with optional specified label, excluding other
Intensity measurements, but retaining all other columns.
"""
label += ".*__\d" if with_multiplicity else ""
dft = df.filter(regex="^(?!Ratio).*$")
... | python | def filter_ratio(df, label="", with_multiplicity=False):
"""
Filter to include only the Ratio values with optional specified label, excluding other
Intensity measurements, but retaining all other columns.
"""
label += ".*__\d" if with_multiplicity else ""
dft = df.filter(regex="^(?!Ratio).*$")
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mfitzp/padua | padua/io.py | read_perseus | def read_perseus(f):
"""
Load a Perseus processed data table
:param f: Source file
:return: Pandas dataframe of imported data
"""
df = pd.read_csv(f, delimiter='\t', header=[0,1,2,3], low_memory=False)
df.columns = pd.MultiIndex.from_tuples([(x,) for x in df.columns.get_level_values(0)])
... | python | def read_perseus(f):
"""
Load a Perseus processed data table
:param f: Source file
:return: Pandas dataframe of imported data
"""
df = pd.read_csv(f, delimiter='\t', header=[0,1,2,3], low_memory=False)
df.columns = pd.MultiIndex.from_tuples([(x,) for x in df.columns.get_level_values(0)])
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mfitzp/padua | padua/io.py | write_perseus | def write_perseus(f, df):
"""
Export a dataframe to Perseus; recreating the format
:param f:
:param df:
:return:
"""
### Generate the Perseus like type index
FIELD_TYPE_MAP = {
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"""
Export a dataframe to Perseus; recreating the format
:param f:
:param df:
:return:
"""
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FIELD_TYPE_MAP = {
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mfitzp/padua | padua/io.py | write_phosphopath_ratio | def write_phosphopath_ratio(df, f, a, *args, **kwargs):
"""
Write out the data frame ratio between two groups
protein-Rsite-multiplicity-timepoint
ID Ratio
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Q6GQQ9-S100-1-1 0.504
Q86YP4-S100-1-1 0.506
Q9H307-S100-1-1 0.508
Q8NEY1-S1000-1-1 0... | python | def write_phosphopath_ratio(df, f, a, *args, **kwargs):
"""
Write out the data frame ratio between two groups
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ID Ratio
Q13619-S10-1-1 0.5
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Q6GQQ9-S100-1-1 0.504
Q86YP4-S100-1-1 0.506
Q9H307-S100-1-1 0.508
Q8NEY1-S1000-1-1 0... | [
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mfitzp/padua | padua/io.py | write_r | def write_r(df, f, sep=",", index_join="@", columns_join="."):
"""
Export dataframe in a format easily importable to R
Index fields are joined with "@" and column fields by "." by default.
:param df:
:param f:
:param index_join:
:param columns_join:
:return:
"""
df = df.copy()
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"""
Export dataframe in a format easily importable to R
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mfitzp/padua | padua/imputation.py | gaussian | def gaussian(df, width=0.3, downshift=-1.8, prefix=None):
"""
Impute missing values by drawing from a normal distribution
:param df:
:param width: Scale factor for the imputed distribution relative to the standard deviation of measured values. Can be a single number or list of one per column.
:para... | python | def gaussian(df, width=0.3, downshift=-1.8, prefix=None):
"""
Impute missing values by drawing from a normal distribution
:param df:
:param width: Scale factor for the imputed distribution relative to the standard deviation of measured values. Can be a single number or list of one per column.
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mfitzp/padua | padua/visualize.py | _pca_scores | def _pca_scores(
scores,
pc1=0,
pc2=1,
fcol=None,
ecol=None,
marker='o',
markersize=30,
label_scores=None,
show_covariance_ellipse=True,
optimize_label_iter=OPTIMIZE_LABEL_ITER_DEFAULT,
**kwargs
):
"""
Plot a scores plot... | python | def _pca_scores(
scores,
pc1=0,
pc2=1,
fcol=None,
ecol=None,
marker='o',
markersize=30,
label_scores=None,
show_covariance_ellipse=True,
optimize_label_iter=OPTIMIZE_LABEL_ITER_DEFAULT,
**kwargs
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mfitzp/padua | padua/visualize.py | modifiedaminoacids | def modifiedaminoacids(df, kind='pie'):
"""
Generate a plot of relative numbers of modified amino acids in source DataFrame.
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"""
Generate a plot of relative numbers of modified amino acids in source DataFrame.
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mfitzp/padua | padua/visualize.py | venn | def venn(df1, df2, df3=None, labels=None, ix1=None, ix2=None, ix3=None, return_intersection=False, fcols=None):
"""
Plot a 2 or 3-part venn diagram showing the overlap between 2 or 3 pandas DataFrames.
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"""
Plot a 2 or 3-part venn diagram showing the overlap between 2 or 3 pandas DataFrames.
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mfitzp/padua | padua/visualize.py | sitespeptidesproteins | def sitespeptidesproteins(df, labels=None, colors=None, site_localization_probability=0.75):
"""
Plot the number of sites, peptides and proteins in the dataset.
Generates a plot with sites, peptides and proteins displayed hierarchically in chevrons.
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"""
Plot the number of sites, peptides and proteins in the dataset.
Generates a plot with sites, peptides and proteins displayed hierarchically in chevrons.
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mfitzp/padua | padua/visualize.py | _areadist | def _areadist(ax, v, xr, c, bins=100, by=None, alpha=1, label=None):
"""
Plot the histogram distribution but as an area plot
"""
y, x = np.histogram(v[~np.isnan(v)], bins)
x = x[:-1]
if by is None:
by = np.zeros((bins,))
ax.fill_between(x, y, by, facecolor=c, alpha=alpha, label=lab... | python | def _areadist(ax, v, xr, c, bins=100, by=None, alpha=1, label=None):
"""
Plot the histogram distribution but as an area plot
"""
y, x = np.histogram(v[~np.isnan(v)], bins)
x = x[:-1]
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mfitzp/padua | padua/visualize.py | hierarchical_timecourse | def hierarchical_timecourse(
df,
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cluster_rows=False,
n_col_clusters=False,
n_row_clusters=False,
fcol=None,
z_score=0,
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return_clusters=False,
rdistance_fn=distance.pdist,
cdi... | python | def hierarchical_timecourse(
df,
cluster_cols=True,
cluster_rows=False,
n_col_clusters=False,
n_row_clusters=False,
fcol=None,
z_score=0,
method='ward',
cmap=cm.PuOr_r,
return_clusters=False,
rdistance_fn=distance.pdist,
cdi... | [
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mfitzp/padua | padua/normalization.py | subtract_column_median | def subtract_column_median(df, prefix='Intensity '):
"""
Apply column-wise normalisation to expression columns.
Default is median transform to expression columns beginning with Intensity
:param df:
:param prefix: The column prefix for expression columns
:return:
"""
df = df.copy()
... | python | def subtract_column_median(df, prefix='Intensity '):
"""
Apply column-wise normalisation to expression columns.
Default is median transform to expression columns beginning with Intensity
:param df:
:param prefix: The column prefix for expression columns
:return:
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mfitzp/padua | padua/utils.py | get_protein_id_list | def get_protein_id_list(df, level=0):
"""
Return a complete list of shortform IDs from a DataFrame
Extract all protein IDs from a dataframe from multiple rows containing
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"""
Return a complete list of shortform IDs from a DataFrame
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mfitzp/padua | padua/utils.py | hierarchical_match | def hierarchical_match(d, k, default=None):
"""
Match a key against a dict, simplifying element at a time
:param df: DataFrame
:type df: pandas.DataFrame
:param level: Level of DataFrame index to extract IDs from
:type level: int or str
:return: hiearchically matched value or default
"... | python | def hierarchical_match(d, k, default=None):
"""
Match a key against a dict, simplifying element at a time
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mfitzp/padua | padua/utils.py | calculate_s0_curve | def calculate_s0_curve(s0, minpval, maxpval, minratio, maxratio, curve_interval=0.1):
"""
Calculate s0 curve for volcano plot.
Taking an min and max p value, and a min and max ratio, calculate an smooth
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The `curve_interval` parameter defines th... | python | def calculate_s0_curve(s0, minpval, maxpval, minratio, maxratio, curve_interval=0.1):
"""
Calculate s0 curve for volcano plot.
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mfitzp/padua | padua/analysis.py | correlation | def correlation(df, rowvar=False):
"""
Calculate column-wise Pearson correlations using ``numpy.ma.corrcoef``
Input data is masked to ignore NaNs when calculating correlations. Data is returned as
a Pandas ``DataFrame`` of column_n x column_n dimensions, with column index copied to
both axes.
... | python | def correlation(df, rowvar=False):
"""
Calculate column-wise Pearson correlations using ``numpy.ma.corrcoef``
Input data is masked to ignore NaNs when calculating correlations. Data is returned as
a Pandas ``DataFrame`` of column_n x column_n dimensions, with column index copied to
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mfitzp/padua | padua/analysis.py | pca | def pca(df, n_components=2, mean_center=False, **kwargs):
"""
Principal Component Analysis, based on `sklearn.decomposition.PCA`
Performs a principal component analysis (PCA) on the supplied dataframe, selecting the first ``n_components`` components
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"""
Principal Component Analysis, based on `sklearn.decomposition.PCA`
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mfitzp/padua | padua/analysis.py | plsda | def plsda(df, a, b, n_components=2, mean_center=False, scale=True, **kwargs):
"""
Partial Least Squares Discriminant Analysis, based on `sklearn.cross_decomposition.PLSRegression`
Performs a binary group partial least squares discriminant analysis (PLS-DA) on the supplied
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"""
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mfitzp/padua | padua/analysis.py | enrichment_from_evidence | def enrichment_from_evidence(dfe, modification="Phospho (STY)"):
"""
Calculate relative enrichment of peptide modifications from evidence.txt.
Taking a modifiedsitepeptides ``DataFrame`` returns the relative enrichment of the specified
modification in the table.
The returned data columns are gener... | python | def enrichment_from_evidence(dfe, modification="Phospho (STY)"):
"""
Calculate relative enrichment of peptide modifications from evidence.txt.
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mfitzp/padua | padua/analysis.py | enrichment_from_msp | def enrichment_from_msp(dfmsp, modification="Phospho (STY)"):
"""
Calculate relative enrichment of peptide modifications from modificationSpecificPeptides.txt.
Taking a modifiedsitepeptides ``DataFrame`` returns the relative enrichment of the specified
modification in the table.
The returned data ... | python | def enrichment_from_msp(dfmsp, modification="Phospho (STY)"):
"""
Calculate relative enrichment of peptide modifications from modificationSpecificPeptides.txt.
Taking a modifiedsitepeptides ``DataFrame`` returns the relative enrichment of the specified
modification in the table.
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mfitzp/padua | padua/analysis.py | sitespeptidesproteins | def sitespeptidesproteins(df, site_localization_probability=0.75):
"""
Generate summary count of modified sites, peptides and proteins in a processed dataset ``DataFrame``.
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"""
Generate summary count of modified sites, peptides and proteins in a processed dataset ``DataFrame``.
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mfitzp/padua | padua/analysis.py | modifiedaminoacids | def modifiedaminoacids(df):
"""
Calculate the number of modified amino acids in supplied ``DataFrame``.
Returns the total of all modifications and the total for each amino acid individually, as an ``int`` and a
``dict`` of ``int``, keyed by amino acid, respectively.
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"""
Calculate the number of modified amino acids in supplied ``DataFrame``.
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mfitzp/padua | padua/process.py | build_index_from_design | def build_index_from_design(df, design, remove_prefix=None, types=None, axis=1, auto_convert_numeric=True, unmatched_columns='index'):
"""
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mfitzp/padua | padua/process.py | build_index_from_labels | def build_index_from_labels(df, indices, remove_prefix=None, types=None, axis=1):
"""
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"""
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mfitzp/padua | padua/process.py | combine_expression_columns | def combine_expression_columns(df, columns_to_combine, remove_combined=True):
"""
Combine expression columns, calculating the mean for 2 columns
:param df: Pandas dataframe
:param columns_to_combine: A list of tuples containing the column names to combine
:return:
"""
df = df.copy()
... | python | def combine_expression_columns(df, columns_to_combine, remove_combined=True):
"""
Combine expression columns, calculating the mean for 2 columns
:param df: Pandas dataframe
:param columns_to_combine: A list of tuples containing the column names to combine
:return:
"""
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mfitzp/padua | padua/process.py | expand_side_table | def expand_side_table(df):
"""
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mfitzp/padua | padua/process.py | apply_experimental_design | def apply_experimental_design(df, f, prefix='Intensity '):
"""
Load the experimental design template from MaxQuant and use it to apply the label names to the data columns.
:param df:
:param f: File path for the experimental design template
:param prefix:
:return: dt
"""
df = df.copy()
... | python | def apply_experimental_design(df, f, prefix='Intensity '):
"""
Load the experimental design template from MaxQuant and use it to apply the label names to the data columns.
:param df:
:param f: File path for the experimental design template
:param prefix:
:return: dt
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mfitzp/padua | padua/process.py | transform_expression_columns | def transform_expression_columns(df, fn=np.log2, prefix='Intensity '):
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mfitzp/padua | padua/process.py | fold_columns_to_rows | def fold_columns_to_rows(df, levels_from=2):
"""
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ECRL/ecabc | ecabc/abc.py | ABC.args | def args(self, args):
'''Set additional arguments to be passed to the fitness function
Args:
args (dict): additional arguments
'''
self._args = args
self._logger.log('debug', 'Args set to {}'.format(args)) | python | def args(self, args):
'''Set additional arguments to be passed to the fitness function
Args:
args (dict): additional arguments
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ECRL/ecabc | ecabc/abc.py | ABC.minimize | def minimize(self, minimize):
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Args:
minimize (bool): if True, minimizes fitness function return value;
if False, minimizes derived score
'''
self._minimize = minimize
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Args:
minimize (bool): if True, minimizes fitness function return value;
if False, minimizes derived score
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ECRL/ecabc | ecabc/abc.py | ABC.num_employers | def num_employers(self, num_employers):
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num_employers (int): number of employer bees
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if num_employers < 2:
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num_employers (int): number of employer bees
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ECRL/ecabc | ecabc/abc.py | ABC.processes | def processes(self, processes):
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processes (int): number of concurrent processes
'''
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processes (int): number of concurrent processes
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ECRL/ecabc | ecabc/abc.py | ABC.create_employers | def create_employers(self):
'''Generate employer bees. This should be called directly after the
ABC is initialized.
'''
self.__verify_ready(True)
employers = []
for i in range(self._num_employers):
employer = EmployerBee(self.__gen_random_values())
... | python | def create_employers(self):
'''Generate employer bees. This should be called directly after the
ABC is initialized.
'''
self.__verify_ready(True)
employers = []
for i in range(self._num_employers):
employer = EmployerBee(self.__gen_random_values())
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ECRL/ecabc | ecabc/abc.py | ABC.run_iteration | def run_iteration(self):
'''Runs a single iteration of the ABC; employer phase -> probability
calculation -> onlooker phase -> check positions
'''
self._employer_phase()
self._calc_probability()
self._onlooker_phase()
self._check_positions() | python | def run_iteration(self):
'''Runs a single iteration of the ABC; employer phase -> probability
calculation -> onlooker phase -> check positions
'''
self._employer_phase()
self._calc_probability()
self._onlooker_phase()
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ECRL/ecabc | ecabc/abc.py | ABC._calc_probability | def _calc_probability(self):
'''Determines the probability that each bee will be chosen during the
onlooker phase; also determines if a new best-performing bee is found
'''
self._logger.log('debug', 'Calculating bee probabilities')
self.__verify_ready()
self._total_score... | python | def _calc_probability(self):
'''Determines the probability that each bee will be chosen during the
onlooker phase; also determines if a new best-performing bee is found
'''
self._logger.log('debug', 'Calculating bee probabilities')
self.__verify_ready()
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Args:
bee (EmployerBee): supplied bee to merge
Returns:
tuple: (score of new position, values of new position, fitness
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'''Shifts a random value for a supplied bee with in accordance with
another random bee's value
Args:
bee (EmployerBee): supplied bee to merge
Returns:
tuple: (score of new position, values of new position, fitness
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'''Moves a bee to a new position if new fitness score is better than
the bee's current fitness score
Args:
bee (EmployerBee): bee to move
new_values (tuple): (new score, new values, new fitness function
return value)
... | python | def _move_bee(self, bee, new_values):
'''Moves a bee to a new position if new fitness score is better than
the bee's current fitness score
Args:
bee (EmployerBee): bee to move
new_values (tuple): (new score, new values, new fitness function
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ECRL/ecabc | ecabc/abc.py | ABC.__update | def __update(self, score, values, error):
'''Update the best score and values if the given score is better than
the current best score
Args:
score (float): new score to evaluate
values (list): new value ranges to evaluate
error (float): new fitness function r... | python | def __update(self, score, values, error):
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score (float): new score to evaluate
values (list): new value ranges to evaluate
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ECRL/ecabc | ecabc/abc.py | ABC.__gen_random_values | def __gen_random_values(self):
'''Generate random values based on supplied value ranges
Returns:
list: random values, one per tunable variable
'''
values = []
if self._value_ranges is None:
self._logger.log(
'crit',
'Must ... | python | def __gen_random_values(self):
'''Generate random values based on supplied value ranges
Returns:
list: random values, one per tunable variable
'''
values = []
if self._value_ranges is None:
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ECRL/ecabc | ecabc/abc.py | ABC.__verify_ready | def __verify_ready(self, creating=False):
'''Some cleanup, ensures that everything is set up properly to avoid
random errors during execution
Args:
creating (bool): True if currently creating employer bees, False
for checking all other operations
'''
... | python | def __verify_ready(self, creating=False):
'''Some cleanup, ensures that everything is set up properly to avoid
random errors during execution
Args:
creating (bool): True if currently creating employer bees, False
for checking all other operations
'''
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ECRL/ecabc | ecabc/abc.py | ABC.import_settings | def import_settings(self, filename):
'''Import settings from a JSON file
Args:
filename (string): name of the file to import from
'''
if not os.path.isfile(filename):
self._logger.log(
'error',
'File: {} not found, continuing with... | python | def import_settings(self, filename):
'''Import settings from a JSON file
Args:
filename (string): name of the file to import from
'''
if not os.path.isfile(filename):
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ECRL/ecabc | ecabc/abc.py | ABC.save_settings | def save_settings(self, filename):
'''Save settings to a JSON file
Arge:
filename (string): name of the file to save to
'''
data = dict()
data['valueRanges'] = self._value_ranges
data['best_values'] = [str(value) for value in self._best_values]
data[... | python | def save_settings(self, filename):
'''Save settings to a JSON file
Arge:
filename (string): name of the file to save to
'''
data = dict()
data['valueRanges'] = self._value_ranges
data['best_values'] = [str(value) for value in self._best_values]
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ECRL/ecabc | ecabc/bees.py | EmployerBee.get_score | def get_score(self, error=None):
'''Calculate bee's fitness score given a value returned by the fitness
function
Args:
error (float): value returned by the fitness function
Returns:
float: derived fitness score
'''
if error is not None:
... | python | def get_score(self, error=None):
'''Calculate bee's fitness score given a value returned by the fitness
function
Args:
error (float): value returned by the fitness function
Returns:
float: derived fitness score
'''
if error is not None:
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foremast/foremast | src/foremast/dns/create_dns.py | SpinnakerDns.create_elb_dns | def create_elb_dns(self, regionspecific=False):
"""Create dns entries in route53.
Args:
regionspecific (bool): The DNS entry should have region on it
Returns:
str: Auto-generated DNS name for the Elastic Load Balancer.
"""
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"""Create dns entries in route53.
Args:
regionspecific (bool): The DNS entry should have region on it
Returns:
str: Auto-generated DNS name for the Elastic Load Balancer.
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foremast/foremast | src/foremast/dns/create_dns.py | SpinnakerDns.create_failover_dns | def create_failover_dns(self, primary_region='us-east-1'):
"""Create dns entries in route53 for multiregion failover setups.
Args:
primary_region (str): primary AWS region for failover
Returns:
Auto-generated DNS name.
"""
dns_record = self.generated.dns(... | python | def create_failover_dns(self, primary_region='us-east-1'):
"""Create dns entries in route53 for multiregion failover setups.
Args:
primary_region (str): primary AWS region for failover
Returns:
Auto-generated DNS name.
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foremast/foremast | src/foremast/elb/format_listeners.py | format_listeners | def format_listeners(elb_settings=None, env='dev', region='us-east-1'):
"""Format ELB Listeners into standard list.
Args:
elb_settings (dict): ELB settings including ELB Listeners to add,
e.g.::
# old
{
"certificate": null,
... | python | def format_listeners(elb_settings=None, env='dev', region='us-east-1'):
"""Format ELB Listeners into standard list.
Args:
elb_settings (dict): ELB settings including ELB Listeners to add,
e.g.::
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foremast/foremast | src/foremast/elb/format_listeners.py | format_cert_name | def format_cert_name(env='', account='', region='', certificate=None):
"""Format the SSL certificate name into ARN for ELB.
Args:
env (str): Account environment name
account (str): Account number for ARN
region (str): AWS Region.
certificate (str): Name of SSL certificate
R... | python | def format_cert_name(env='', account='', region='', certificate=None):
"""Format the SSL certificate name into ARN for ELB.
Args:
env (str): Account environment name
account (str): Account number for ARN
region (str): AWS Region.
certificate (str): Name of SSL certificate
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foremast/foremast | src/foremast/elb/format_listeners.py | generate_custom_cert_name | def generate_custom_cert_name(env='', region='', account='', certificate=None):
"""Generate a custom TLS Cert name based on a template.
Args:
env (str): Account environment name
region (str): AWS Region.
account (str): Account number for ARN.
certificate (str): Name of SSL certi... | python | def generate_custom_cert_name(env='', region='', account='', certificate=None):
"""Generate a custom TLS Cert name based on a template.
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env (str): Account environment name
region (str): AWS Region.
account (str): Account number for ARN.
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foremast/foremast | src/foremast/slacknotify/__main__.py | main | def main():
"""Send Slack notification to a configured channel."""
logging.basicConfig(format=LOGGING_FORMAT)
log = logging.getLogger(__name__)
parser = argparse.ArgumentParser()
add_debug(parser)
add_app(parser)
add_env(parser)
add_properties(parser)
args = parser.parse_args()
... | python | def main():
"""Send Slack notification to a configured channel."""
logging.basicConfig(format=LOGGING_FORMAT)
log = logging.getLogger(__name__)
parser = argparse.ArgumentParser()
add_debug(parser)
add_app(parser)
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foremast/foremast | src/foremast/destroyer.py | main | def main(): # noqa
"""Attempt to fully destroy AWS Resources for a Spinnaker Application."""
logging.basicConfig(format=LOGGING_FORMAT)
parser = argparse.ArgumentParser(description=main.__doc__)
add_debug(parser)
add_app(parser)
args = parser.parse_args()
if args.debug == logging.DEBUG:
... | python | def main(): # noqa
"""Attempt to fully destroy AWS Resources for a Spinnaker Application."""
logging.basicConfig(format=LOGGING_FORMAT)
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foremast/foremast | src/foremast/pipeline/construct_pipeline_block.py | check_provider_healthcheck | def check_provider_healthcheck(settings, default_provider='Discovery'):
"""Set Provider Health Check when specified.
Returns:
collections.namedtuple: **ProviderHealthCheck** with attributes:
* providers (list): Providers set to use native Health Check.
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foremast/foremast | src/foremast/pipeline/construct_pipeline_block.py | get_template_name | def get_template_name(env, pipeline_type):
"""Generates the correct template name based on pipeline type
Args:
env (str): environment to generate templates for
pipeline_type (str): Type of pipeline like ec2 or lambda
Returns:
str: Name of template
"""
pipeline_base = 'pipel... | python | def get_template_name(env, pipeline_type):
"""Generates the correct template name based on pipeline type
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env (str): environment to generate templates for
pipeline_type (str): Type of pipeline like ec2 or lambda
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str: Name of template
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foremast/foremast | src/foremast/pipeline/construct_pipeline_block.py | ec2_pipeline_setup | def ec2_pipeline_setup(
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pipeline_type='',
region='',
region_subnets=None,
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generated=None,
project='',
settings=None,
env='',
pipeline_type='',
region='',
region_subnets=None,
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foremast/foremast | src/foremast/pipeline/create_pipeline_manual.py | SpinnakerPipelineManual.create_pipeline | def create_pipeline(self):
"""Use JSON files to create Pipelines."""
pipelines = self.settings['pipeline']['pipeline_files']
self.log.info('Uploading manual Pipelines: %s', pipelines)
lookup = FileLookup(git_short=self.generated.gitlab()['main'], runway_dir=self.runway_dir)
for... | python | def create_pipeline(self):
"""Use JSON files to create Pipelines."""
pipelines = self.settings['pipeline']['pipeline_files']
self.log.info('Uploading manual Pipelines: %s', pipelines)
lookup = FileLookup(git_short=self.generated.gitlab()['main'], runway_dir=self.runway_dir)
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foremast/foremast | src/foremast/pipeline/__main__.py | main | def main():
"""Creates a pipeline in Spinnaker"""
logging.basicConfig(format=LOGGING_FORMAT)
log = logging.getLogger(__name__)
parser = argparse.ArgumentParser()
add_debug(parser)
add_app(parser)
add_properties(parser)
parser.add_argument('-b', '--base', help='Base AMI name to use, e.g.... | python | def main():
"""Creates a pipeline in Spinnaker"""
logging.basicConfig(format=LOGGING_FORMAT)
log = logging.getLogger(__name__)
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add_debug(parser)
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foremast/foremast | src/foremast/configs/outputs.py | convert_ini | def convert_ini(config_dict):
"""Convert _config_dict_ into a list of INI formatted strings.
Args:
config_dict (dict): Configuration dictionary to be flattened.
Returns:
(list) Lines to be written to a file in the format of KEY1_KEY2=value.
"""
config_lines = []
for env, confi... | python | def convert_ini(config_dict):
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config_dict (dict): Configuration dictionary to be flattened.
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foremast/foremast | src/foremast/configs/outputs.py | write_variables | def write_variables(app_configs=None, out_file='', git_short=''):
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"""Append _application.json_ configs to _out_file_, .exports, and .json.
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foremast/foremast | src/foremast/utils/get_sns_subscriptions.py | get_sns_subscriptions | def get_sns_subscriptions(app_name, env, region):
"""List SNS lambda subscriptions.
Returns:
list: List of Lambda subscribed SNS ARNs.
"""
session = boto3.Session(profile_name=env, region_name=region)
sns_client = session.client('sns')
lambda_alias_arn = get_lambda_alias_arn(app=app_n... | python | def get_sns_subscriptions(app_name, env, region):
"""List SNS lambda subscriptions.
Returns:
list: List of Lambda subscribed SNS ARNs.
"""
session = boto3.Session(profile_name=env, region_name=region)
sns_client = session.client('sns')
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foremast/foremast | src/foremast/awslambda/cloudwatch_log_event/destroy_cloudwatch_log_event/destroy_cloudwatch_log_event.py | destroy_cloudwatch_log_event | def destroy_cloudwatch_log_event(app='', env='dev', region=''):
"""Destroy Cloudwatch log event.
Args:
app (str): Spinnaker Application name.
env (str): Deployment environment.
region (str): AWS region.
Returns:
bool: True upon successful completion.
"""
session = b... | python | def destroy_cloudwatch_log_event(app='', env='dev', region=''):
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Args:
app (str): Spinnaker Application name.
env (str): Deployment environment.
region (str): AWS region.
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bool: True upon successful completion.
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foremast/foremast | src/foremast/app/create_app.py | SpinnakerApp.get_accounts | def get_accounts(self, provider='aws'):
"""Get Accounts added to Spinnaker.
Args:
provider (str): What provider to find accounts for.
Returns:
list: list of dicts of Spinnaker credentials matching _provider_.
Raises:
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"""Get Accounts added to Spinnaker.
Args:
provider (str): What provider to find accounts for.
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foremast/foremast | src/foremast/app/create_app.py | SpinnakerApp.create_app | def create_app(self):
"""Send a POST to spinnaker to create a new application with class variables.
Raises:
AssertionError: Application creation failed.
"""
self.appinfo['accounts'] = self.get_accounts()
self.log.debug('Pipeline Config\n%s', pformat(self.pipeline_con... | python | def create_app(self):
"""Send a POST to spinnaker to create a new application with class variables.
Raises:
AssertionError: Application creation failed.
"""
self.appinfo['accounts'] = self.get_accounts()
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"variables",
"."
] | fb70f29b8ce532f061685a17d120486e47b215ba | https://github.com/foremast/foremast/blob/fb70f29b8ce532f061685a17d120486e47b215ba/src/foremast/app/create_app.py#L84-L97 | train |
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