pythonPrograms/BarcodeGroupMatch.py at master · marcsze/pythonPrograms · GitHub

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#! python

# A quick program that matches the asssigns the group based on the barcode sequence when the barcode is stored in

# the fastq file as part of the findex or rindex but not on the sequence itself.

# It will create a group file and if the barcode is not found then it will assign a group name of "none"

# to the sequence.

# Proper usage is as follows:

# python BarcodeGroupMatch.py <sequenceAndBarcodeFile> <oligoFile> <outputfilename> <"Full" or "Partial">

# Load the needed modules for the program

import sys

# Read in a Command arguments for files to match

# Input other instructions from here

def commandLine():

commands = sys.argv

inputfile = commands[1]

oligofile = commands[2]

outputfile = commands[3]

selection = commands[4]

return inputfile, oligofile, outputfile, selection

# Reads in the data and creates a dictionary

def createDataArray(inputfile, n):

inputfile = open(inputfile, 'r')

print("Reading in Data.....")

SeqBarDict = {}

if n == 'name':

for line in inputfile:

name, barcode = line.split('\t')

barcodeStrip = barcode.strip('\n')

SeqBarDict[name] = barcodeStrip

if n == 'oligo':

for line in inputfile:

name, barcode, group = line.split('\t')

groupStrip = group.strip('\n')

SeqBarDict[barcode] = groupStrip

inputfile.close()

return SeqBarDict

# Create function to find matches and if it does not match add a none to it

def matchData(SeqBarDict, BarGroupDict):

matchedDict = {}

print("Matching Sequence to Barcode.....")

for i in SeqBarDict:

try:

bartoMatch = SeqBarDict[i]

foundGroup = BarGroupDict[bartoMatch]

matchedDict[i] = foundGroup

except KeyError:

matchedDict[i] = 'none'

return matchedDict

#Print out group file

def makeGroupfile(matchedDict, outputfile, selection):

outfile = open(outputfile, 'w')

print("Making Group file......")

if selection == "Full":

for i in matchedDict:

group = matchedDict[i]

print("{0}\t{1}".format(i, group), end ='\n', file = outfile)

else:

for i in matchedDict:

group = matchedDict[i]

if group != "none":

print("{0}\t{1}".format(i, group), end ='\n', file = outfile)

outfile.close()

# Run the Program

def main():

inputfile, oligofile, outputfile, selection = commandLine()

SeqBarDict = createDataArray(inputfile, "name")

BarGroupDict = createDataArray(oligofile, "oligo")

matchedDict = matchData(SeqBarDict, BarGroupDict)

makeGroupfile(matchedDict, outputfile, selection)

if __name__ == '__main__': main()

pythonPrograms/BarcodeGroupMatch.py at master · marcsze/pythonPrograms · GitHub

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