NewPythonPrograms/compareDoc.py at master · marcsze/NewPythonPrograms · GitHub

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#! python

# New program to compare two different files and output a number of columns on the

# data infromation of samples that are the same

# Uses the certain convertToList.py programs to edit the existing text file to make

# it more amenable for downstream use

# Read in necessary programs and functions

import sys

from convertToList import readData, identifySamples

# Read in a Command arguments for the program

# Input other instructions from here

def commandLine():

commands = sys.argv

textToConvert = commands[1]

pattern = commands[2]

mappingFile = commands[3]

return textToConvert, pattern, mappingFile

# Read in test data as a dictionary to modify file as needed

def readTestFile(mappingFile, pattern):

data = open(mappingFile, 'r')

testDict = {}

x = 0

for line in data:

if x != 0:

sampleID, barcode, linker, group = line.split("\t")

if pattern in group:

testDict[group.strip('\n')] = sampleID

x = x + 1

return testDict

# Make the comparison between the data and test data

def compareData(dataList, testDict):

noMatchList = []

YESMatchDict = {}

for i, group in enumerate(dataList):

try:

sample = testDict[group]

YESMatchDict[group] = sample

except KeyError:

noMatchList.append(group)

return YESMatchDict, noMatchList

def main():

# Need to change this so that existing commandLine is what is read.

textToConvert, pattern, mappingFile = commandLine()

dataList = readData(textToConvert)

goodData = identifySamples(dataList, pattern)

testDict = readTestFile(mappingFile, pattern)

YESMatchDict, noMatchList = compareData(dataList, testDict)

print(YESMatchDict)

if __name__ == '__main__': main()

NewPythonPrograms/compareDoc.py at master · marcsze/NewPythonPrograms · GitHub

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