idx int64 0 63k | question stringlengths 61 4.03k | target stringlengths 6 1.23k |
|---|---|---|
49,900 | def connect ( self ) : self . serial = serial . Serial ( port = self . port , baudrate = self . baudrate , timeout = self . timeout ) self . alive = True self . rxThread = threading . Thread ( target = self . _readLoop ) self . rxThread . daemon = True self . rxThread . start ( ) | Connects to the device and starts the read thread |
49,901 | def close ( self ) : self . alive = False self . rxThread . join ( ) self . serial . close ( ) | Stops the read thread waits for it to exit cleanly then closes the underlying serial port |
49,902 | def _readLoop ( self ) : try : readTermSeq = list ( self . RX_EOL_SEQ ) readTermLen = len ( readTermSeq ) rxBuffer = [ ] while self . alive : data = self . serial . read ( 1 ) if data != '' : rxBuffer . append ( data ) if rxBuffer [ - readTermLen : ] == readTermSeq : line = '' . join ( rxBuffer [ : - readTermLen ] ) rx... | Read thread main loop Reads lines from the connected device |
49,903 | def _decodeTimestamp ( byteIter ) : dateStr = decodeSemiOctets ( byteIter , 7 ) timeZoneStr = dateStr [ - 2 : ] return datetime . strptime ( dateStr [ : - 2 ] , '%y%m%d%H%M%S' ) . replace ( tzinfo = SmsPduTzInfo ( timeZoneStr ) ) | Decodes a 7 - octet timestamp |
49,904 | def decodeUcs2 ( byteIter , numBytes ) : userData = [ ] i = 0 try : while i < numBytes : userData . append ( unichr ( ( next ( byteIter ) << 8 ) | next ( byteIter ) ) ) i += 2 except StopIteration : pass return '' . join ( userData ) | Decodes UCS2 - encoded text from the specified byte iterator up to a maximum of numBytes |
49,905 | def encode ( self ) : result = bytearray ( ) result . append ( self . id ) result . append ( self . dataLength ) result . extend ( self . data ) return result | Encodes this IE and returns the resulting bytes |
49,906 | def parseArgsPy26 ( ) : from gsmtermlib . posoptparse import PosOptionParser , Option parser = PosOptionParser ( description = 'Simple script for sending SMS messages' ) parser . add_option ( '-i' , '--port' , metavar = 'PORT' , help = 'port to which the GSM modem is connected; a number or a device name.' ) parser . ad... | Argument parser for Python 2 . 6 |
49,907 | def lineMatching ( regexStr , lines ) : regex = re . compile ( regexStr ) for line in lines : m = regex . match ( line ) if m : return m else : return None | Searches through the specified list of strings and returns the regular expression match for the first line that matches the specified regex string or None if no match was found |
49,908 | def lineMatchingPattern ( pattern , lines ) : for line in lines : m = pattern . match ( line ) if m : return m else : return None | Searches through the specified list of strings and returns the regular expression match for the first line that matches the specified pre - compiled regex pattern or None if no match was found |
49,909 | def allLinesMatchingPattern ( pattern , lines ) : result = [ ] for line in lines : m = pattern . match ( line ) if m : result . append ( m ) return result | Like lineMatchingPattern but returns all lines that match the specified pattern |
49,910 | def clean ( decrypted : bytes ) -> str : r last = decrypted [ - 1 ] if isinstance ( last , int ) : return decrypted [ : - last ] . decode ( 'utf8' ) return decrypted [ : - ord ( last ) ] . decode ( 'utf8' ) | r Strip padding from decrypted value . |
49,911 | def set_pattern_step_setpoint ( self , patternnumber , stepnumber , setpointvalue ) : _checkPatternNumber ( patternnumber ) _checkStepNumber ( stepnumber ) _checkSetpointValue ( setpointvalue , self . setpoint_max ) address = _calculateRegisterAddress ( 'setpoint' , patternnumber , stepnumber ) self . write_register ( ... | Set the setpoint value for a step . |
49,912 | def get_pattern_step_time ( self , patternnumber , stepnumber ) : _checkPatternNumber ( patternnumber ) _checkStepNumber ( stepnumber ) address = _calculateRegisterAddress ( 'time' , patternnumber , stepnumber ) return self . read_register ( address , 0 ) | Get the step time . |
49,913 | def set_pattern_step_time ( self , patternnumber , stepnumber , timevalue ) : _checkPatternNumber ( patternnumber ) _checkStepNumber ( stepnumber ) _checkTimeValue ( timevalue , self . time_max ) address = _calculateRegisterAddress ( 'time' , patternnumber , stepnumber ) self . write_register ( address , timevalue , 0 ... | Set the step time . |
49,914 | def get_pattern_actual_step ( self , patternnumber ) : _checkPatternNumber ( patternnumber ) address = _calculateRegisterAddress ( 'actualstep' , patternnumber ) return self . read_register ( address , 0 ) | Get the actual step parameter for a given pattern . |
49,915 | def set_pattern_actual_step ( self , patternnumber , value ) : _checkPatternNumber ( patternnumber ) _checkStepNumber ( value ) address = _calculateRegisterAddress ( 'actualstep' , patternnumber ) self . write_register ( address , value , 0 ) | Set the actual step parameter for a given pattern . |
49,916 | def get_pattern_additional_cycles ( self , patternnumber ) : _checkPatternNumber ( patternnumber ) address = _calculateRegisterAddress ( 'cycles' , patternnumber ) return self . read_register ( address ) | Get the number of additional cycles for a given pattern . |
49,917 | def set_pattern_additional_cycles ( self , patternnumber , value ) : _checkPatternNumber ( patternnumber ) minimalmodbus . _checkInt ( value , minvalue = 0 , maxvalue = 99 , description = 'number of additional cycles' ) address = _calculateRegisterAddress ( 'cycles' , patternnumber ) self . write_register ( address , v... | Set the number of additional cycles for a given pattern . |
49,918 | def get_pattern_link_topattern ( self , patternnumber ) : _checkPatternNumber ( patternnumber ) address = _calculateRegisterAddress ( 'linkpattern' , patternnumber ) return self . read_register ( address ) | Get the linked pattern value for a given pattern . |
49,919 | def get_all_pattern_variables ( self , patternnumber ) : _checkPatternNumber ( patternnumber ) outputstring = '' for stepnumber in range ( 8 ) : outputstring += 'SP{0}: {1} Time{0}: {2}\n' . format ( stepnumber , self . get_pattern_step_setpoint ( patternnumber , stepnumber ) , self . get_pattern_step_time ( patternnu... | Get all variables for a given pattern at one time . |
49,920 | def set_all_pattern_variables ( self , patternnumber , sp0 , ti0 , sp1 , ti1 , sp2 , ti2 , sp3 , ti3 , sp4 , ti4 , sp5 , ti5 , sp6 , ti6 , sp7 , ti7 , actual_step , additional_cycles , link_pattern ) : _checkPatternNumber ( patternnumber ) self . set_pattern_step_setpoint ( patternnumber , 0 , sp0 ) self . set_pattern_... | Set all variables for a given pattern at one time . |
49,921 | def close ( self ) : if VERBOSE : _print_out ( '\nDummy_serial: Closing port\n' ) if not self . _isOpen : raise IOError ( 'Dummy_serial: The port is already closed' ) self . _isOpen = False self . port = None | Close a port on dummy_serial . |
49,922 | def write ( self , inputdata ) : if VERBOSE : _print_out ( '\nDummy_serial: Writing to port. Given:' + repr ( inputdata ) + '\n' ) if sys . version_info [ 0 ] > 2 : if not type ( inputdata ) == bytes : raise TypeError ( 'The input must be type bytes. Given:' + repr ( inputdata ) ) inputstring = str ( inputdata , encodi... | Write to a port on dummy_serial . |
49,923 | def read ( self , numberOfBytes ) : if VERBOSE : _print_out ( '\nDummy_serial: Reading from port (max length {!r} bytes)' . format ( numberOfBytes ) ) if numberOfBytes < 0 : raise IOError ( 'Dummy_serial: The numberOfBytes to read must not be negative. Given: {!r}' . format ( numberOfBytes ) ) if not self . _isOpen : r... | Read from a port on dummy_serial . |
49,924 | def _embedPayload ( slaveaddress , mode , functioncode , payloaddata ) : _checkSlaveaddress ( slaveaddress ) _checkMode ( mode ) _checkFunctioncode ( functioncode , None ) _checkString ( payloaddata , description = 'payload' ) firstPart = _numToOneByteString ( slaveaddress ) + _numToOneByteString ( functioncode ) + pay... | Build a request from the slaveaddress the function code and the payload data . |
49,925 | def _extractPayload ( response , slaveaddress , mode , functioncode ) : BYTEPOSITION_FOR_ASCII_HEADER = 0 BYTEPOSITION_FOR_SLAVEADDRESS = 0 BYTEPOSITION_FOR_FUNCTIONCODE = 1 NUMBER_OF_RESPONSE_STARTBYTES = 2 NUMBER_OF_CRC_BYTES = 2 NUMBER_OF_LRC_BYTES = 1 BITNUMBER_FUNCTIONCODE_ERRORINDICATION = 7 MINIMAL_RESPONSE_LENG... | Extract the payload data part from the slave s response . |
49,926 | def _predictResponseSize ( mode , functioncode , payloadToSlave ) : MIN_PAYLOAD_LENGTH = 4 BYTERANGE_FOR_GIVEN_SIZE = slice ( 2 , 4 ) NUMBER_OF_PAYLOAD_BYTES_IN_WRITE_CONFIRMATION = 4 NUMBER_OF_PAYLOAD_BYTES_FOR_BYTECOUNTFIELD = 1 RTU_TO_ASCII_PAYLOAD_FACTOR = 2 NUMBER_OF_RTU_RESPONSE_STARTBYTES = 2 NUMBER_OF_RTU_RESPO... | Calculate the number of bytes that should be received from the slave . |
49,927 | def _calculate_minimum_silent_period ( baudrate ) : _checkNumerical ( baudrate , minvalue = 1 , description = 'baudrate' ) BITTIMES_PER_CHARACTERTIME = 11 MINIMUM_SILENT_CHARACTERTIMES = 3.5 bittime = 1 / float ( baudrate ) return bittime * BITTIMES_PER_CHARACTERTIME * MINIMUM_SILENT_CHARACTERTIMES | Calculate the silent period length to comply with the 3 . 5 character silence between messages . |
49,928 | def _numToTwoByteString ( value , numberOfDecimals = 0 , LsbFirst = False , signed = False ) : _checkNumerical ( value , description = 'inputvalue' ) _checkInt ( numberOfDecimals , minvalue = 0 , description = 'number of decimals' ) _checkBool ( LsbFirst , description = 'LsbFirst' ) _checkBool ( signed , description = ... | Convert a numerical value to a two - byte string possibly scaling it . |
49,929 | def _twoByteStringToNum ( bytestring , numberOfDecimals = 0 , signed = False ) : _checkString ( bytestring , minlength = 2 , maxlength = 2 , description = 'bytestring' ) _checkInt ( numberOfDecimals , minvalue = 0 , description = 'number of decimals' ) _checkBool ( signed , description = 'signed parameter' ) formatcode... | Convert a two - byte string to a numerical value possibly scaling it . |
49,930 | def _pack ( formatstring , value ) : _checkString ( formatstring , description = 'formatstring' , minlength = 1 ) try : result = struct . pack ( formatstring , value ) except : errortext = 'The value to send is probably out of range, as the num-to-bytestring conversion failed.' errortext += ' Value: {0!r} Struct format... | Pack a value into a bytestring . |
49,931 | def _unpack ( formatstring , packed ) : _checkString ( formatstring , description = 'formatstring' , minlength = 1 ) _checkString ( packed , description = 'packed string' , minlength = 1 ) if sys . version_info [ 0 ] > 2 : packed = bytes ( packed , encoding = 'latin1' ) try : value = struct . unpack ( formatstring , pa... | Unpack a bytestring into a value . |
49,932 | def _hexencode ( bytestring , insert_spaces = False ) : _checkString ( bytestring , description = 'byte string' ) separator = '' if not insert_spaces else ' ' byte_representions = [ ] for c in bytestring : byte_representions . append ( '{0:02X}' . format ( ord ( c ) ) ) return separator . join ( byte_representions ) . ... | Convert a byte string to a hex encoded string . |
49,933 | def _hexdecode ( hexstring ) : _checkString ( hexstring , description = 'hexstring' ) if len ( hexstring ) % 2 != 0 : raise ValueError ( 'The input hexstring must be of even length. Given: {!r}' . format ( hexstring ) ) if sys . version_info [ 0 ] > 2 : by = bytes ( hexstring , 'latin1' ) try : return str ( binascii . ... | Convert a hex encoded string to a byte string . |
49,934 | def _bitResponseToValue ( bytestring ) : _checkString ( bytestring , description = 'bytestring' , minlength = 1 , maxlength = 1 ) RESPONSE_ON = '\x01' RESPONSE_OFF = '\x00' if bytestring == RESPONSE_ON : return 1 elif bytestring == RESPONSE_OFF : return 0 else : raise ValueError ( 'Could not convert bit response to a v... | Convert a response string to a numerical value . |
49,935 | def _createBitpattern ( functioncode , value ) : _checkFunctioncode ( functioncode , [ 5 , 15 ] ) _checkInt ( value , minvalue = 0 , maxvalue = 1 , description = 'inputvalue' ) if functioncode == 5 : if value == 0 : return '\x00\x00' else : return '\xff\x00' elif functioncode == 15 : if value == 0 : return '\x00' else ... | Create the bit pattern that is used for writing single bits . |
49,936 | def _twosComplement ( x , bits = 16 ) : _checkInt ( bits , minvalue = 0 , description = 'number of bits' ) _checkInt ( x , description = 'input' ) upperlimit = 2 ** ( bits - 1 ) - 1 lowerlimit = - 2 ** ( bits - 1 ) if x > upperlimit or x < lowerlimit : raise ValueError ( 'The input value is out of range. Given value is... | Calculate the two s complement of an integer . |
49,937 | def _setBitOn ( x , bitNum ) : _checkInt ( x , minvalue = 0 , description = 'input value' ) _checkInt ( bitNum , minvalue = 0 , description = 'bitnumber' ) return x | ( 1 << bitNum ) | Set bit bitNum to True . |
49,938 | def _calculateCrcString ( inputstring ) : _checkString ( inputstring , description = 'input CRC string' ) register = 0xFFFF for char in inputstring : register = ( register >> 8 ) ^ _CRC16TABLE [ ( register ^ ord ( char ) ) & 0xFF ] return _numToTwoByteString ( register , LsbFirst = True ) | Calculate CRC - 16 for Modbus . |
49,939 | def _calculateLrcString ( inputstring ) : _checkString ( inputstring , description = 'input LRC string' ) register = 0 for character in inputstring : register += ord ( character ) lrc = ( ( register ^ 0xFF ) + 1 ) & 0xFF lrcString = _numToOneByteString ( lrc ) return lrcString | Calculate LRC for Modbus . |
49,940 | def _checkMode ( mode ) : if not isinstance ( mode , str ) : raise TypeError ( 'The {0} should be a string. Given: {1!r}' . format ( "mode" , mode ) ) if mode not in [ MODE_RTU , MODE_ASCII ] : raise ValueError ( "Unreconized Modbus mode given. Must be 'rtu' or 'ascii' but {0!r} was given." . format ( mode ) ) | Check that the Modbus mode is valie . |
49,941 | def _checkFunctioncode ( functioncode , listOfAllowedValues = [ ] ) : FUNCTIONCODE_MIN = 1 FUNCTIONCODE_MAX = 127 _checkInt ( functioncode , FUNCTIONCODE_MIN , FUNCTIONCODE_MAX , description = 'functioncode' ) if listOfAllowedValues is None : return if not isinstance ( listOfAllowedValues , list ) : raise TypeError ( '... | Check that the given functioncode is in the listOfAllowedValues . |
49,942 | def _checkResponseByteCount ( payload ) : POSITION_FOR_GIVEN_NUMBER = 0 NUMBER_OF_BYTES_TO_SKIP = 1 _checkString ( payload , minlength = 1 , description = 'payload' ) givenNumberOfDatabytes = ord ( payload [ POSITION_FOR_GIVEN_NUMBER ] ) countedNumberOfDatabytes = len ( payload ) - NUMBER_OF_BYTES_TO_SKIP if givenNumbe... | Check that the number of bytes as given in the response is correct . |
49,943 | def _checkResponseRegisterAddress ( payload , registeraddress ) : _checkString ( payload , minlength = 2 , description = 'payload' ) _checkRegisteraddress ( registeraddress ) BYTERANGE_FOR_STARTADDRESS = slice ( 0 , 2 ) bytesForStartAddress = payload [ BYTERANGE_FOR_STARTADDRESS ] receivedStartAddress = _twoByteStringT... | Check that the start adress as given in the response is correct . |
49,944 | def _checkResponseNumberOfRegisters ( payload , numberOfRegisters ) : _checkString ( payload , minlength = 4 , description = 'payload' ) _checkInt ( numberOfRegisters , minvalue = 1 , maxvalue = 0xFFFF , description = 'numberOfRegisters' ) BYTERANGE_FOR_NUMBER_OF_REGISTERS = slice ( 2 , 4 ) bytesForNumberOfRegisters = ... | Check that the number of written registers as given in the response is correct . |
49,945 | def _checkResponseWriteData ( payload , writedata ) : _checkString ( payload , minlength = 4 , description = 'payload' ) _checkString ( writedata , minlength = 2 , maxlength = 2 , description = 'writedata' ) BYTERANGE_FOR_WRITEDATA = slice ( 2 , 4 ) receivedWritedata = payload [ BYTERANGE_FOR_WRITEDATA ] if receivedWri... | Check that the write data as given in the response is correct . |
49,946 | def _checkString ( inputstring , description , minlength = 0 , maxlength = None ) : if not isinstance ( description , str ) : raise TypeError ( 'The description should be a string. Given: {0!r}' . format ( description ) ) if not isinstance ( inputstring , str ) : raise TypeError ( 'The {0} should be a string. Given: {1... | Check that the given string is valid . |
49,947 | def _checkInt ( inputvalue , minvalue = None , maxvalue = None , description = 'inputvalue' ) : if not isinstance ( description , str ) : raise TypeError ( 'The description should be a string. Given: {0!r}' . format ( description ) ) if not isinstance ( inputvalue , ( int , long ) ) : raise TypeError ( 'The {0} must be... | Check that the given integer is valid . |
49,948 | def _checkNumerical ( inputvalue , minvalue = None , maxvalue = None , description = 'inputvalue' ) : if not isinstance ( description , str ) : raise TypeError ( 'The description should be a string. Given: {0!r}' . format ( description ) ) if not isinstance ( inputvalue , ( int , long , float ) ) : raise TypeError ( 'T... | Check that the given numerical value is valid . |
49,949 | def _checkBool ( inputvalue , description = 'inputvalue' ) : _checkString ( description , minlength = 1 , description = 'description string' ) if not isinstance ( inputvalue , bool ) : raise TypeError ( 'The {0} must be boolean. Given: {1!r}' . format ( description , inputvalue ) ) | Check that the given inputvalue is a boolean . |
49,950 | def _getDiagnosticString ( ) : text = '\n## Diagnostic output from minimalmodbus ## \n\n' text += 'Minimalmodbus version: ' + __version__ + '\n' text += 'Minimalmodbus status: ' + __status__ + '\n' text += 'File name (with relative path): ' + __file__ + '\n' text += 'Full file path: ' + os . path . abspath ( __file__ )... | Generate a diagnostic string showing the module version the platform current directory etc . |
49,951 | def read_bit ( self , registeraddress , functioncode = 2 ) : _checkFunctioncode ( functioncode , [ 1 , 2 ] ) return self . _genericCommand ( functioncode , registeraddress ) | Read one bit from the slave . |
49,952 | def write_bit ( self , registeraddress , value , functioncode = 5 ) : _checkFunctioncode ( functioncode , [ 5 , 15 ] ) _checkInt ( value , minvalue = 0 , maxvalue = 1 , description = 'input value' ) self . _genericCommand ( functioncode , registeraddress , value ) | Write one bit to the slave . |
49,953 | def read_register ( self , registeraddress , numberOfDecimals = 0 , functioncode = 3 , signed = False ) : _checkFunctioncode ( functioncode , [ 3 , 4 ] ) _checkInt ( numberOfDecimals , minvalue = 0 , maxvalue = 10 , description = 'number of decimals' ) _checkBool ( signed , description = 'signed' ) return self . _gener... | Read an integer from one 16 - bit register in the slave possibly scaling it . |
49,954 | def write_register ( self , registeraddress , value , numberOfDecimals = 0 , functioncode = 16 , signed = False ) : _checkFunctioncode ( functioncode , [ 6 , 16 ] ) _checkInt ( numberOfDecimals , minvalue = 0 , maxvalue = 10 , description = 'number of decimals' ) _checkBool ( signed , description = 'signed' ) _checkNum... | Write an integer to one 16 - bit register in the slave possibly scaling it . |
49,955 | def read_float ( self , registeraddress , functioncode = 3 , numberOfRegisters = 2 ) : _checkFunctioncode ( functioncode , [ 3 , 4 ] ) _checkInt ( numberOfRegisters , minvalue = 2 , maxvalue = 4 , description = 'number of registers' ) return self . _genericCommand ( functioncode , registeraddress , numberOfRegisters = ... | Read a floating point number from the slave . |
49,956 | def write_float ( self , registeraddress , value , numberOfRegisters = 2 ) : _checkNumerical ( value , description = 'input value' ) _checkInt ( numberOfRegisters , minvalue = 2 , maxvalue = 4 , description = 'number of registers' ) self . _genericCommand ( 16 , registeraddress , value , numberOfRegisters = numberOfReg... | Write a floating point number to the slave . |
49,957 | def read_string ( self , registeraddress , numberOfRegisters = 16 , functioncode = 3 ) : _checkFunctioncode ( functioncode , [ 3 , 4 ] ) _checkInt ( numberOfRegisters , minvalue = 1 , description = 'number of registers for read string' ) return self . _genericCommand ( functioncode , registeraddress , numberOfRegisters... | Read a string from the slave . |
49,958 | def write_string ( self , registeraddress , textstring , numberOfRegisters = 16 ) : _checkInt ( numberOfRegisters , minvalue = 1 , description = 'number of registers for write string' ) _checkString ( textstring , 'input string' , minlength = 1 , maxlength = 2 * numberOfRegisters ) self . _genericCommand ( 16 , registe... | Write a string to the slave . |
49,959 | def write_registers ( self , registeraddress , values ) : if not isinstance ( values , list ) : raise TypeError ( 'The "values parameter" must be a list. Given: {0!r}' . format ( values ) ) _checkInt ( len ( values ) , minvalue = 1 , description = 'length of input list' ) self . _genericCommand ( 16 , registeraddress ,... | Write integers to 16 - bit registers in the slave . |
49,960 | def _communicate ( self , request , number_of_bytes_to_read ) : _checkString ( request , minlength = 1 , description = 'request' ) _checkInt ( number_of_bytes_to_read ) if self . debug : _print_out ( '\nMinimalModbus debug mode. Writing to instrument (expecting {} bytes back): {!r} ({})' . format ( number_of_bytes_to_r... | Talk to the slave via a serial port . |
49,961 | def _playsoundWin ( sound , block = True ) : from ctypes import c_buffer , windll from random import random from time import sleep from sys import getfilesystemencoding def winCommand ( * command ) : buf = c_buffer ( 255 ) command = ' ' . join ( command ) . encode ( getfilesystemencoding ( ) ) errorCode = int ( windll ... | Utilizes windll . winmm . Tested and known to work with MP3 and WAVE on Windows 7 with Python 2 . 7 . Probably works with more file formats . Probably works on Windows XP thru Windows 10 . Probably works with all versions of Python . |
49,962 | def _playsoundOSX ( sound , block = True ) : from AppKit import NSSound from Foundation import NSURL from time import sleep if '://' not in sound : if not sound . startswith ( '/' ) : from os import getcwd sound = getcwd ( ) + '/' + sound sound = 'file://' + sound url = NSURL . URLWithString_ ( sound ) nssound = NSSoun... | Utilizes AppKit . NSSound . Tested and known to work with MP3 and WAVE on OS X 10 . 11 with Python 2 . 7 . Probably works with anything QuickTime supports . Probably works on OS X 10 . 5 and newer . Probably works with all versions of Python . |
49,963 | def _playsoundNix ( sound , block = True ) : if not block : raise NotImplementedError ( "block=False cannot be used on this platform yet" ) import os try : from urllib . request import pathname2url except ImportError : from urllib import pathname2url import gi gi . require_version ( 'Gst' , '1.0' ) from gi . repository... | Play a sound using GStreamer . |
49,964 | def remove_rows_matching ( df , column , match ) : df = df . copy ( ) mask = df [ column ] . values != match return df . iloc [ mask , : ] | Return a DataFrame with rows where column values match match are removed . |
49,965 | def remove_rows_containing ( df , column , match ) : df = df . copy ( ) mask = [ match not in str ( v ) for v in df [ column ] . values ] return df . iloc [ mask , : ] | Return a DataFrame with rows where column values containing match are removed . |
49,966 | def filter_localization_probability ( df , threshold = 0.75 ) : df = df . copy ( ) localization_probability_mask = df [ 'Localization prob' ] . values >= threshold return df . iloc [ localization_probability_mask , : ] | Remove rows with a localization probability below 0 . 75 |
49,967 | def minimum_valid_values_in_any_group ( df , levels = None , n = 1 , invalid = np . nan ) : df = df . copy ( ) if levels is None : if 'Group' in df . columns . names : levels = [ df . columns . names . index ( 'Group' ) ] if invalid is np . nan : dfx = ~ np . isnan ( df ) else : dfx = df != invalid dfc = dfx . astype (... | Filter DataFrame by at least n valid values in at least one group . |
49,968 | def search ( df , match , columns = [ 'Proteins' , 'Protein names' , 'Gene names' ] ) : df = df . copy ( ) dft = df . reset_index ( ) mask = np . zeros ( ( dft . shape [ 0 ] , ) , dtype = bool ) idx = [ 'Proteins' , 'Protein names' , 'Gene names' ] for i in idx : if i in dft . columns : mask = mask | np . array ( [ mat... | Search for a given string in a set of columns in a processed DataFrame . |
49,969 | def filter_select_columns_intensity ( df , prefix , columns ) : return df . filter ( regex = '^(%s.+|%s)$' % ( prefix , '|' . join ( columns ) ) ) | Filter dataframe to include specified columns retaining any Intensity columns . |
49,970 | def filter_intensity ( df , label = "" , with_multiplicity = False ) : label += ".*__\d" if with_multiplicity else "" dft = df . filter ( regex = "^(?!Intensity).*$" ) dfi = df . filter ( regex = '^(.*Intensity.*%s.*__\d)$' % label ) return pd . concat ( [ dft , dfi ] , axis = 1 ) | Filter to include only the Intensity values with optional specified label excluding other Intensity measurements but retaining all other columns . |
49,971 | def filter_ratio ( df , label = "" , with_multiplicity = False ) : label += ".*__\d" if with_multiplicity else "" dft = df . filter ( regex = "^(?!Ratio).*$" ) dfr = df . filter ( regex = '^(.*Ratio.*%s)$' % label ) return pd . concat ( [ dft , dfr ] , axis = 1 ) | Filter to include only the Ratio values with optional specified label excluding other Intensity measurements but retaining all other columns . |
49,972 | def read_perseus ( f ) : 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 ) ] ) return df | Load a Perseus processed data table |
49,973 | def write_perseus ( f , df ) : FIELD_TYPE_MAP = { 'Amino acid' : 'C' , 'Charge' : 'C' , 'Reverse' : 'C' , 'Potential contaminant' : 'C' , 'Multiplicity' : 'C' , 'Localization prob' : 'N' , 'PEP' : 'N' , 'Score' : 'N' , 'Delta score' : 'N' , 'Score for localization' : 'N' , 'Mass error [ppm]' : 'N' , 'Intensity' : 'N' ,... | Export a dataframe to Perseus ; recreating the format |
49,974 | def write_phosphopath_ratio ( df , f , a , * args , ** kwargs ) : timepoint_idx = kwargs . get ( 'timepoint_idx' , None ) proteins = [ get_protein_id ( k ) for k in df . index . get_level_values ( 'Proteins' ) ] amino_acids = df . index . get_level_values ( 'Amino acid' ) positions = _get_positions ( df ) multiplicity ... | Write out the data frame ratio between two groups protein - Rsite - multiplicity - timepoint ID Ratio Q13619 - S10 - 1 - 1 0 . 5 Q9H3Z4 - S10 - 1 - 1 0 . 502 Q6GQQ9 - S100 - 1 - 1 0 . 504 Q86YP4 - S100 - 1 - 1 0 . 506 Q9H307 - S100 - 1 - 1 0 . 508 Q8NEY1 - S1000 - 1 - 1 0 . 51 Q13541 - S101 - 1 - 1 0 . 512 O95785 - S10... |
49,975 | def write_r ( df , f , sep = "," , index_join = "@" , columns_join = "." ) : df = df . copy ( ) df . index = [ "@" . join ( [ str ( s ) for s in v ] ) for v in df . index . values ] df . columns = [ "." . join ( [ str ( s ) for s in v ] ) for v in df . index . values ] df . to_csv ( f , sep = sep ) | Export dataframe in a format easily importable to R |
49,976 | def gaussian ( df , width = 0.3 , downshift = - 1.8 , prefix = None ) : df = df . copy ( ) imputed = df . isnull ( ) if prefix : mask = np . array ( [ l . startswith ( prefix ) for l in df . columns . values ] ) mycols = np . arange ( 0 , df . shape [ 1 ] ) [ mask ] else : mycols = np . arange ( 0 , df . shape [ 1 ] ) ... | Impute missing values by drawing from a normal distribution |
49,977 | 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 ) : fig = plt . figure ( figsize = ( 8 , 8 ) ) ax = fig . add_subplot ( 1 , 1 , 1 ) levels = [ ... | Plot a scores plot for two principal components as AxB scatter plot . |
49,978 | def modifiedaminoacids ( df , kind = 'pie' ) : colors = [ '#6baed6' , '#c6dbef' , '#bdbdbd' ] total_aas , quants = analysis . modifiedaminoacids ( df ) df = pd . DataFrame ( ) for a , n in quants . items ( ) : df [ a ] = [ n ] df . sort_index ( axis = 1 , inplace = True ) if kind == 'bar' or kind == 'both' : ax1 = df .... | Generate a plot of relative numbers of modified amino acids in source DataFrame . |
49,979 | def venn ( df1 , df2 , df3 = None , labels = None , ix1 = None , ix2 = None , ix3 = None , return_intersection = False , fcols = None ) : try : import matplotlib_venn as mplv except ImportError : raise ImportError ( "To plot venn diagrams, install matplotlib-venn package: pip install matplotlib-venn" ) plt . gcf ( ) . ... | Plot a 2 or 3 - part venn diagram showing the overlap between 2 or 3 pandas DataFrames . |
49,980 | def sitespeptidesproteins ( df , labels = None , colors = None , site_localization_probability = 0.75 ) : fig = plt . figure ( figsize = ( 4 , 6 ) ) ax = fig . add_subplot ( 1 , 1 , 1 ) shift = 0.5 values = analysis . sitespeptidesproteins ( df , site_localization_probability ) if labels is None : labels = [ 'Sites (Cl... | Plot the number of sites peptides and proteins in the dataset . |
49,981 | def _areadist ( ax , v , xr , c , bins = 100 , by = None , alpha = 1 , label = None ) : 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 = label ) return y | Plot the histogram distribution but as an area plot |
49,982 | 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 , cdistance_fn = distance . pdist , xlabel = 'Timepoint' , ylabel... | Hierarchical clustering of samples across timecourse experiment . |
49,983 | def subtract_column_median ( df , prefix = 'Intensity ' ) : df = df . copy ( ) df . replace ( [ np . inf , - np . inf ] , np . nan , inplace = True ) mask = [ l . startswith ( prefix ) for l in df . columns . values ] df . iloc [ : , mask ] = df . iloc [ : , mask ] - df . iloc [ : , mask ] . median ( axis = 0 ) return ... | Apply column - wise normalisation to expression columns . |
49,984 | def get_protein_id_list ( df , level = 0 ) : protein_list = [ ] for s in df . index . get_level_values ( level ) : protein_list . extend ( get_protein_ids ( s ) ) return list ( set ( protein_list ) ) | Return a complete list of shortform IDs from a DataFrame |
49,985 | def hierarchical_match ( d , k , default = None ) : if d is None : return default if type ( k ) != list and type ( k ) != tuple : k = [ k ] for n , _ in enumerate ( k ) : key = tuple ( k [ 0 : len ( k ) - n ] ) if len ( key ) == 1 : key = key [ 0 ] try : d [ key ] except : pass else : return d [ key ] return default | Match a key against a dict simplifying element at a time |
49,986 | def calculate_s0_curve ( s0 , minpval , maxpval , minratio , maxratio , curve_interval = 0.1 ) : mminpval = - np . log10 ( minpval ) mmaxpval = - np . log10 ( maxpval ) maxpval_adjust = mmaxpval - mminpval ax0 = ( s0 + maxpval_adjust * minratio ) / maxpval_adjust edge_offset = ( maxratio - ax0 ) % curve_interval max_x ... | Calculate s0 curve for volcano plot . |
49,987 | def correlation ( df , rowvar = False ) : df = df . copy ( ) maskv = np . ma . masked_where ( np . isnan ( df . values ) , df . values ) cdf = np . ma . corrcoef ( maskv , rowvar = False ) cdf = pd . DataFrame ( np . array ( cdf ) ) cdf . columns = df . columns cdf . index = df . columns cdf = cdf . sort_index ( level ... | Calculate column - wise Pearson correlations using numpy . ma . corrcoef |
49,988 | def pca ( df , n_components = 2 , mean_center = False , ** kwargs ) : if not sklearn : assert ( 'This library depends on scikit-learn (sklearn) to perform PCA analysis' ) from sklearn . decomposition import PCA df = df . copy ( ) df [ np . isnan ( df ) ] = 0 if mean_center : mean = np . mean ( df . values , axis = 0 ) ... | Principal Component Analysis based on sklearn . decomposition . PCA |
49,989 | def plsda ( df , a , b , n_components = 2 , mean_center = False , scale = True , ** kwargs ) : if not sklearn : assert ( 'This library depends on scikit-learn (sklearn) to perform PLS-DA' ) from sklearn . cross_decomposition import PLSRegression df = df . copy ( ) df [ np . isnan ( df ) ] = 0 if mean_center : mean = np... | Partial Least Squares Discriminant Analysis based on sklearn . cross_decomposition . PLSRegression |
49,990 | def enrichment_from_evidence ( dfe , modification = "Phospho (STY)" ) : dfe = dfe . reset_index ( ) . set_index ( 'Experiment' ) dfe [ 'Modifications' ] = np . array ( [ modification in m for m in dfe [ 'Modifications' ] ] ) dfe = dfe . set_index ( 'Modifications' , append = True ) dfes = dfe . sum ( axis = 0 , level =... | Calculate relative enrichment of peptide modifications from evidence . txt . |
49,991 | def enrichment_from_msp ( dfmsp , modification = "Phospho (STY)" ) : dfmsp [ 'Modifications' ] = np . array ( [ modification in m for m in dfmsp [ 'Modifications' ] ] ) dfmsp = dfmsp . set_index ( [ 'Modifications' ] ) dfmsp = dfmsp . filter ( regex = 'Intensity ' ) dfmsp [ dfmsp == 0 ] = np . nan df_r = dfmsp . sum ( ... | Calculate relative enrichment of peptide modifications from modificationSpecificPeptides . txt . |
49,992 | def sitespeptidesproteins ( df , site_localization_probability = 0.75 ) : sites = filters . filter_localization_probability ( df , site_localization_probability ) [ 'Sequence window' ] peptides = set ( df [ 'Sequence window' ] ) proteins = set ( [ str ( p ) . split ( ';' ) [ 0 ] for p in df [ 'Proteins' ] ] ) return le... | Generate summary count of modified sites peptides and proteins in a processed dataset DataFrame . |
49,993 | def modifiedaminoacids ( df ) : amino_acids = list ( df [ 'Amino acid' ] . values ) aas = set ( amino_acids ) quants = { } for aa in aas : quants [ aa ] = amino_acids . count ( aa ) total_aas = len ( amino_acids ) return total_aas , quants | Calculate the number of modified amino acids in supplied DataFrame . |
49,994 | def build_index_from_design ( df , design , remove_prefix = None , types = None , axis = 1 , auto_convert_numeric = True , unmatched_columns = 'index' ) : df = df . copy ( ) if 'Label' not in design . index . names : design = design . set_index ( 'Label' ) if remove_prefix is None : remove_prefix = [ ] if type ( remove... | Build a MultiIndex from a design table . |
49,995 | def build_index_from_labels ( df , indices , remove_prefix = None , types = None , axis = 1 ) : df = df . copy ( ) if remove_prefix is None : remove_prefix = [ ] if types is None : types = { } idx = [ df . index , df . columns ] [ axis ] indexes = [ ] for l in idx . get_level_values ( 0 ) : for s in remove_prefix : l =... | Build a MultiIndex from a list of labels and matching regex |
49,996 | def combine_expression_columns ( df , columns_to_combine , remove_combined = True ) : df = df . copy ( ) for ca , cb in columns_to_combine : df [ "%s_(x+y)/2_%s" % ( ca , cb ) ] = ( df [ ca ] + df [ cb ] ) / 2 if remove_combined : for ca , cb in columns_to_combine : df . drop ( [ ca , cb ] , inplace = True , axis = 1 )... | Combine expression columns calculating the mean for 2 columns |
49,997 | def expand_side_table ( df ) : df = df . copy ( ) idx = df . index . names df . reset_index ( inplace = True ) def strip_multiplicity ( df ) : df . columns = [ c [ : - 4 ] for c in df . columns ] return df def strip_multiple ( s ) : for sr in [ ' 1' , ' 2' , ' 3' ] : if s . endswith ( sr ) : s = s [ : - 4 ] return s ba... | Perform equivalent of expand side table in Perseus by folding Multiplicity columns down onto duplicate rows |
49,998 | def apply_experimental_design ( df , f , prefix = 'Intensity ' ) : df = df . copy ( ) edt = pd . read_csv ( f , sep = '\t' , header = 0 ) edt . set_index ( 'Experiment' , inplace = True ) new_column_labels = [ ] for l in df . columns . values : try : l = edt . loc [ l . replace ( prefix , '' ) ] [ 'Name' ] except ( Ind... | Load the experimental design template from MaxQuant and use it to apply the label names to the data columns . |
49,999 | def transform_expression_columns ( df , fn = np . log2 , prefix = 'Intensity ' ) : df = df . copy ( ) mask = np . array ( [ l . startswith ( prefix ) for l in df . columns . values ] ) df . iloc [ : , mask ] = fn ( df . iloc [ : , mask ] ) df . replace ( [ np . inf , - np . inf ] , np . nan , inplace = True ) return df | Apply transformation to expression columns . |
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