#!/usr/bin/python3
import argparse
import os
import re
import sys
import state
import timedStates
import score
import globalVariables
import pprint
import csv
import upper
import pickle
# Convert to UpperCase
upper.toUpper(globalVariables.inputcsv)
# Replace T with U
os.system('sed -i s/T/U/g '+globalVariables.inputcsv)
def main():
count=1
outputList=[]
globalVariables.rawScoreMatrix = pickle.load(open(globalVariables.scoreMatrixFile,"rb"))
globalVariables.states = pickle.load(open(globalVariables.statesFile,"rb"))
globalVariables.timedStates = pickle.load(open(globalVariables.timedStatesFile,"rb"))
# print(globalVariables.rawScoreMatrix)
# print(globalVariables.states)
# print(globalVariables.timedStates)
with open(globalVariables.inputcsv, 'r') as csvfile:
reader = csv.DictReader(csvfile)
#!/usr/bin/python3
import argparse
import os
import re
import sys
import state
import timedStates
import score
import globalVariables
import pprint
import csv
import upper
import pickle
# Convert to UpperCase
upper.toUpper(globalVariables.csvFile)
# Replace T with U
os.system('sed -i s/T/U/g ' + globalVariables.csvFile)
def main():
# for later looping
score.initRawScoreMatrix()
with open(globalVariables.csvFile, 'r') as csvfile:
reader = csv.DictReader(csvfile)
names = reader.fieldnames
for row in reader:
# Assuming that the sequences will be in the first two rows
# Compute probabilities with sequence 1 and reverse of sequence 2
doStuff(row[names[0]], row[names[1]][::-1])
globalVariables.timedStates = timedStates.initTimedStates(
#!/usr/bin/python3
import argparse
import os
import re
import sys
import state
import timedStates
import score
import globalVariables
import pprint
import csv
import upper
import pickle
# Convert to UpperCase
upper.toUpper(globalVariables.inputcsv)
# Replace T with U
os.system('sed -i s/T/U/g ' + globalVariables.inputcsv)
def main():
count = 1
outputList = []
globalVariables.rawScoreMatrix = pickle.load(
open(globalVariables.scoreMatrixFile, "rb"))
globalVariables.states = pickle.load(open(globalVariables.statesFile,
"rb"))
globalVariables.timedStates = pickle.load(
open(globalVariables.timedStatesFile, "rb"))
# print(globalVariables.rawScoreMatrix)
#!/usr/bin/python3
import argparse
import os
import re
import sys
import state
import timedStates
import score
import globalVariables
import pprint
import csv
import upper
import pickle
# Convert to UpperCase
upper.toUpper(globalVariables.csvFile)
# Replace T with U
os.system('sed -i s/T/U/g '+globalVariables.csvFile)
def main():
# for later looping
score.initRawScoreMatrix()
with open(globalVariables.csvFile, 'r') as csvfile:
reader = csv.DictReader(csvfile)
names=reader.fieldnames
for row in reader:
# Assuming that the sequences will be in the first two rows
# Compute probabilities with sequence 1 and reverse of sequence 2
doStuff(row[names[0]],row[names[1]][::-1])
globalVariables.timedStates=timedStates.initTimedStates(globalVariables.states)
pickle.dump(globalVariables.states,open(globalVariables.statesFile,"wb"))