def __init__(self, inarg, Stype=FS.SIMILARITY, new=True):
self.thisown = 0
# First check if we are passing the SWIG wrapped type.
if isinstance(inarg, FS_Smatrix):
if new:
self.this = FS.Smatrix_copy(inarg)
self.thisown = 1
else:
self.this = inarg
self.thisown = 1
elif isinstance(inarg, str):
# Load from file
self.this = FS.Smatrix_load(inarg)
self.thisown = 1
# Dictionary - Biopython matrix
elif isinstance(inarg, dict):
self.this = FS.new_Smatrix(inarg, Stype)
self.thisown = 1
# Instance of ScoreMatrix
elif isinstance(inarg, ScoreMatrix):
self.this = FS.Smatrix_copy(inarg.this)
self.thisown = 1
else:
raise TypeError, "Constructor only accepts"\
" a filename, a dictionary"\
" and an instance of ScoreMatrix."
self.alphabet = FS.Smatrix_alphabet_get(self)
self.mean = self._calc_mean()
def matrix_conv(self, seq=""):
if (self.conv_type & 1) == POS:
return ProfileMatrix(FS.Smatrix_matrix_conv(self, seq),
new=False)
else:
return ScoreMatrix(FS.Smatrix_matrix_conv(self, seq),
new=False)
def __init__(self, inarg, Stype=FS.SIMILARITY, new=True):
self.thisown = 0
if type(inarg) is types.StringType:
if new == True:
# Load from file
self.this = FS.Smatrix_load(inarg)
self.thisown = 1
else:
# SWIG string
self.this = inarg
self.thisown = 1
# Dictionary - Biopython matrix
elif isinstance(inarg, dict):
self.this = FS.new_Smatrix(inarg, Stype)
self.thisown = 1
# Instance of ScoreMatrix
elif isinstance(inarg, ScoreMatrix):
self.this = FS.Smatrix_copy(inarg)
self.thisown = 1
else:
raise TypeError, "Constructor only accepts"
" a filename, a dictionary"
" and an instance of ScoreMatrix."
self.alphabet = FS.Smatrix_alphabet_get(self)
self.mean = self._calc_mean()
def __init__(self, inarg, Stype=FS.SIMILARITY, new=True):
self.thisown = 0
if isinstance(inarg, FS_Smatrix):
if new:
self.this = FS.Smatrix_copy(inarg)
self.thisown = 1
else:
self.this = inarg
self.thisown = 1
elif isinstance(inarg, list):
# List - Biopython PSSM
self.this = FS.Smatrix_pssm(inarg)
self.thisown = 1
elif isinstance(inarg, ProfileMatrix):
# Instance of ProfileMatrix
self.this = FS.Smatrix_copy(inarg.this)
self.thisown = 1
else:
raise TypeError, "Constructor only accepts"\
" a Biopython PSSM"\
" and an instance of ProfileMatrix."
self.mean = self._calc_mean()
self.alphabet = FS.Smatrix_alphabet_get(self)
self._len = FS.Smatrix_len_get(self)
self.qseq = FS.Smatrix_qseq_get(self)
def __init__(self, db_name, new=True, own=True):
self.thisown = 0
if new == True:
self.this = FS.new_db(db_name)
self.thisown = 1
elif own == True:
# SWIG string - thisown = 1
self.this = db_name
self.thisown = 1
else:
# SWIG string - thisown = 0
self.this = db_name
self.thisown = 0
pd.options.display.max_colwidth = 100
pd.options.display.max_columns = 10
# ##### Examples: FS #####
# Load workout-history table to dataframe
# Note the 'u' in front, denoting a unicode string
collections = [
u'workout-history',
u'can-eat-options',
u'exercises',
u'food-items',
]
firestore = FS.FS()
# Get all exercises that have a string instead of a DocRef
wh = collections[0]
firestore.loadCollection(wh)
workoutHistory = firestore.collections[wh]
df = pd.DataFrame.from_dict(data)
filtered = df[df['Exercise'].apply(isinstance, args=(str, ))]
# # Normalize Data
# Update "Hex deadlift", "Shoulder press", "Bent over row" to title case.
filtered['Exercise'] # show data
# Define a function that checks for title case. Must have value for all use cases.
def isNotTitle(string):
def __del__(self):
if self.thisown:
FS.delete_Smatrix(self)
def matrix_conv(self):
return ProfileMatrix(FS.Smatrix_matrix_conv(self, ''),
new=False)
SIMILARITY = FS.SIMILARITY
DISTANCE = FS.DISTANCE
# Conversion values
POS = FS.POS
QUASI = FS.QUASI
MAX = FS.MAX
AVG = FS.AVG
# SWIG types - I don't know how to get them directly so I am using constructors
# to get their instances. Then, I get types from these instances. Ideally, I
# would use the new -builtin flag to SWIG and forgo all these wrapper
# files. However, this would break existing code and require extensive testing
_tmp_Smatrix = FS.new_Smatrix({('A', 'A'): 0}, FS.SIMILARITY)
FS_Smatrix = type(_tmp_Smatrix)
FS.delete_Smatrix(_tmp_Smatrix)
# Dummy matrix classes
class SubstitutionMatrix(dict):
"""
Biopython matrix as a new class.
"""
pass
class MatrixColumn(object):
def __init__(self, col, this, alphabet):
self._col = col
def get_frag(self, i, a, b):
return FS.db_get_frag(self, i, a, b)
def get_seq(self, i):
return FS.db_get_seq(self, i)
def range_conv(self, seq, r):
return FS.Smatrix_range_conv(self, seq, r)
def eval_score(self, seq1, seq2):
return FS.Smatrix_eval_score(self, seq1, seq2)
def fprint(fp=sys.stdout):
return FS.Smatrix_fprint(self, fp)
def __str__(self):
return FS.Smatrix___str__(self)
def __del__(self):
if self.thisown:
FS.delete_Smatrix(self)
def __del__(self):
if self.thisown:
FS.delete_db(self)
def eval_score(self, seq1):
seq2 = 'X'*len(seq1)
return FS.Smatrix_eval_score(self, seq1, seq2)
def get_def(self, i):
return FS.db_get_def(self, i)
def range_conv(self, r):
seq = 'X'*self._len
return FS.Smatrix_range_conv(self, seq, r)
## Check if result contains all required data
#if result[0] == 0: lastresult[0] = resultContainsAllOf( result[1], failifnot )
if lastresult[0] != 0 and not cancelonerror: return (lastresult[0], lastresult[1], fallbacklist )
config["lastOutput"] = lastresult[1]
return [lastresult[0], lastresult[1], fallbacklist]
############################
# Main cycle of the program
if __name__ == "__main__":
FS.setLogging( logFileName = config['DEFAULT_LOG'], logLevel=config['DEFAULT_LOGLEVEL'] )
logger = logging.getLogger()
parseArgv( config, logger )
#conf = FS.ConfigStorage( confAddr=config['DEFAULT_CONFIG'], actionName=config['ACTION'] )
#conf = FS.ConfigStorage( confAddr=config['DEFAULT_CONFIG'], actionName=config['ACTION'] )
executor = CommandExecutor( config=config, execFunc=ExecLib.execAction )
logger.debug("\nChecking which action is choosen:")
#DLib.updateCurrentFile( ovaparams["VMname"], CurrentStatus )
result = 0
if config['ACTION'] and ( not config['LIST_ACTIONS'] and not config['DONT_EXECUTE']):
logger.debug("\tThe ACTION \"%s\" is set, while LIST_ACTIONS is not set" % config['ACTION'])
try:
#executor.runAction( config=conf, action=config['ACTION'] )
import FS
import time
if __name__ == "__main__":
fil = FS.FileShareClass()
print(fil.start_fileShare("C:/users/harsh/desktop"))
time.sleep(20)
fil.stopFileShare()
