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

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#! python

# First attempt at using a Kmer based approach to identify contamination.

# Load the needed modules for the program

import sys, re

# Read in a Command arguments for files to match

# Input other instructions from here

def commandLine():

commands = sys.argv

fastafile = commands[1]

length = int(commands[2])

return fastafile, length

# Read in data and create dictionary

def makeDataArray(inputfile, type):

inputfile = open(inputfile, 'r')

if type == "fasta":

# Create specific environment variables

x = 1

names = []

sequence = []

DataDict = {}

# Read data in and create a dictionary

for line in inputfile:

if x%2 != 0:

newLine = re.sub('>', '', line)

names.append(newLine.strip('\t\n'))

else:

sequence.append(line.strip('\n'))

x = x + 1

inputfile.close()

for i, seqName in enumerate(names):

DataDict[seqName] = sequence[i]

# deal with data that is a group file

elif type == "group":

DataDict = {}

for line in inputfile:

seqName, group = line.split('\t')

DataDict[seqName] = group.strip('\n')

# deal with data that is a map file

else:

DataDict = {}

for line in inputfile:

number, seqname = line.split('\t')

DataDict[number] = seqname.strip('\n')

return DataDict

# Function to generate total Kmers

def generateKmersList(sequence, length):

tempKmerList = []

total = len(sequence)

for j,nucleotide in enumerate(sequence):

if j+length > total-1: break

else:

kmerCheck = sequence[j:j+length]

tempKmerList.append(kmerCheck)

return tempKmerList

# Function to remove duplicates from website

# http://www.dotnetperls.com/duplicates-python

def removeDups(tempKmerList):

output = []

seen = set()

for value in tempKmerList:

# If value has not been encountered yet,

# ... add it to both list and set.

if value not in seen:

output.append(value)

seen.add(value)

return output

#Function to get total unique kmers in a given dictionary

def getTotalKmers(fastaDict, length):

kmerNumDict = {}

for i in fastaDict:

sequence = fastaDict[i]

tempKmerList = generateKmersList(sequence, length)

output = removeDups(tempKmerList)

kmerNumDict[i] = len(output)

return kmerNumDict

# Look at what Kmers are highly represented across sequences

# Store the Kmers

# Store the number of times each kmer comes up

# Probably looking for something that shows up in all sequences

# Run the main program

def main():

fastafile, length = commandLine()

fastaDict = makeDataArray(fastafile, "fasta")

kmerNumDict = getTotalKmers(fastaDict, length)

print(kmerNumDict)

if __name__ == '__main__': main()

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

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