This script takes sequenom data and makes plink files

seqtoplink.py

print '\nBuongiorno\n'

print "WELCOME! This script will take sequenom data and make plink files"

resultsFile = open("mappedSeqResults.txt", "r")
resultsMatrix = [[0 for col in range(0)] for row in range(0)]

for line in resultsFile:
	inputInfo = line.split()
	resultsMatrix.append(inputInfo)

#####################################################################

mapFile = open("sample.map", "r")
mapMatrix = [[0 for col in range(0)] for row in range(0)]
mapList = []
n = 0

for line in mapFile:
	inputInfo = line.split()
	mapMatrix.append(inputInfo)
	n = n+1
	
for line in mapMatrix: mapList.append(line[1])
print n

#####################################################################

samplesFile = open("sample.list", "r")
samplesList = []
for line in samplesFile: 
	sampleInfo = line.split()	# get rid of weird formatting
	samplesList.append(sampleInfo[0])

#####################################################################

pedMatrix = [[0 for col in range(0)] for row in range(0)]

count = 0	
for samplesLine in samplesList:
	pedLine = ["00"] * (n+6)
	pedLine[0] = samplesLine
	pedLine[1] = samplesLine
	pedLine[2] = 0
	pedLine[3] = 0
	pedLine[4] = 1
	pedLine[5] = 0

	for resultsLine in resultsMatrix: 
		if resultsLine[0] == pedLine[0]: 
			for mapLine in mapList:
				if resultsLine[2] == mapLine: 
					mapIndex = mapList.index(resultsLine[2]) + 6
					pedLine[mapIndex] = resultsLine[1]
	pedMatrix.append(pedLine)
	
#####################################################################

	
outputFile = "sample.ped"
output = open(outputFile,"w")

for line in pedMatrix:
	for item in line:
		if isinstance(item,str):
			if len(item) == 2: output.write(item[0]+"\t"+item[1]+"\t")
			else: output.write(str(item)+"\t")
		else: output.write(str(item)+"\t")
	output.write("\n")
	
	#for line in pedMatrix:
#	output.write(line[0]+"\t"+line[1]+"\t"+line[2]+"\n")