#! python

# New program to compare or find samples from two different files and output a

# 3 columns of information on the data of samples that are in both files. Uses

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

# amenable for downstream use. The three columnas that are outputed are as follows

# sequencingID, GroupID, file found in.

# An example of how to use this program is below:

## python compareDoc.py samplesToMatch.txt "FD" sample.txt -t output.txt

## samplesToMatch.txt is the file containing samples you want to check

## "FD" can be any term but this is the pattern you are selecting out for in samplesToMatch.txt

## sample.txt is the file you are searching for samples in

## -t moniker "t" if this is the first file you have searched

## output.txt is the name of the ouput file

# 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]

start = commands[4]

outputfile = commands[5]

return textToConvert, pattern, mappingFile, start, outputfile

# 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

# This function will output a tab-delimited text file of the samples

def saveFindings(YESMatchDict, mappingFile, start, outputfile):

#change to 'a' for appending to file rather than write (w)

outfile = open(outputfile, 'a')

if "t" in start:

print("{0}\t{1}\t{2}".format("SequencingID", "SampleID", "MapFile"),

end='\n', file=outfile)

for i in YESMatchDict:

sample = YESMatchDict[i]

print("{0}\t{1}\t{2}".format(sample, i, mappingFile),

end ='\n', file = outfile)

outfile.close()

# Run the overall program

def main():

textToConvert, pattern, mappingFile, start, outputfile = commandLine()

dataList = readData(textToConvert)

goodData = identifySamples(dataList, pattern)

testDict = readTestFile(mappingFile, pattern)

YESMatchDict, noMatchList = compareData(dataList, testDict)

saveFindings(YESMatchDict, mappingFile, start, outputfile)

if __name__ == '__main__': main()