import os, sys, glob, math
import utilities
from operator import itemgetter, attrgetter
inFilePath = sys.argv[1]
expression = sys.argv[2]
reverse = sys.argv[3] == "reverse"
numHeaderRows = int(sys.argv[4])
outFilePath = sys.argv[5]
data = utilities.readMatrixFromFile(inFilePath)
headerRows = []
for i in range(numHeaderRows):
headerRows.append(data.pop(0))
data = map(lambda x: eval("x + [" + expression + "]"), data)
data.sort(key=itemgetter(len(data[0])-1), reverse=reverse)
data = [x[:-1] for x in data]
utilities.writeMatrixToFile(headerRows + data, outFilePath)
import os, sys, glob, shutil
import utilities
decoderFilePath = sys.argv[1]
ccleRawAllDirPath = sys.argv[2]
gskRawAllDirPath = sys.argv[3]
ccleRawSelectedDirPath = sys.argv[4]
gskRawSelectedDirPath = sys.argv[5]
decoderData = utilities.readMatrixFromFile(decoderFilePath)
decoderData.pop(0)
decoderFileDict = {}
decoderNameDict = {}
for row in decoderData:
gskFileName = row[1]
ccleFileName = row[4]
name = row[0] + "_" + row[8] + "_" + row[9] + "_" + row[10]
name = name.replace(" ", "")
decoderFileDict[ccleFileName] = decoderFileDict.setdefault(ccleFileName, []) + [gskFileName]
decoderNameDict[ccleFileName] = decoderNameDict.setdefault(ccleFileName, []) + [name]
for ccleFileName in decoderFileDict:
name = decoderNameDict[ccleFileName][0]
print name
shutil.copy(ccleRawAllDirPath + "/" + ccleFileName + ".CEL", ccleRawSelectedDirPath + "/" + name + ".CEL")
gskFileName = decoderFileDict[ccleFileName][0]
import os, sys, glob
import utilities
inFilePath = sys.argv[1]
numHeaderRows = int(sys.argv[2])
colIndex = int(sys.argv[3])
numPlaces = sys.argv[4]
outFilePath = sys.argv[5]
numberFormatOption = "g"
if len(sys.argv) > 6:
numberFormatOption = sys.argv[6]
data = utilities.readMatrixFromFile(inFilePath)
def isNumber(x):
try:
float(x)
return True
except:
return False
for i in range(numHeaderRows, len(data)):
if isNumber(data[i][colIndex]):
modValue = ("%." + numPlaces + numberFormatOption) % float(
data[i][colIndex])
else:
modValue = data[i][colIndex]
if len(data[i][colIndex]) > int(numPlaces):
import os, sys, glob
import utilities
symbolsFilePath = sys.argv[1]
entrezGenesSymbolsFilePath = sys.argv[2]
entrezGenesSynonymsFilePath = sys.argv[3]
outFilePath = sys.argv[4]
symbols = utilities.readVectorFromFile(symbolsFilePath)
entrezGenesSymbolsData = utilities.readMatrixFromFile(
entrezGenesSymbolsFilePath)
entrezGenesSymbolsDict = {}
for row in entrezGenesSymbolsData:
entrezGenesSymbolsDict[row[1]] = row[0]
entrezGenesSynonymsData = utilities.readMatrixFromFile(
entrezGenesSynonymsFilePath)
entrezGenesSynonymsDict = {}
for row in entrezGenesSynonymsData:
for synonym in row[1].split("|"):
entrezGenesSynonymsDict[synonym] = entrezGenesSynonymsDict.setdefault(
synonym, []) + [row[0]]
outFile = open(outFilePath, 'w')
for symbol in symbols:
if entrezGenesSymbolsDict.has_key(symbol):
entrezID = entrezGenesSymbolsDict[symbol]
else:
if entrezGenesSynonymsDict.has_key(symbol):
entrezIDs = entrezGenesSynonymsDict[symbol]
import os, sys, glob
import utilities
inFilePath1 = sys.argv[1]
inFilePath2 = sys.argv[2]
outFilePath = sys.argv[3]
hasHeader = True
if len(sys.argv) > 4:
hasHeader = sys.argv[4] == "True"
data1 = utilities.readMatrixFromFile(inFilePath1)
data2 = utilities.readMatrixFromFile(inFilePath2)
if hasHeader:
header1 = data1.pop(0)
header2 = data2.pop(0)
if len(header2) == len(data2[0]):
header2.pop(0)
headerCombined = header1 + header2
data1Dict = {}
for row in data1:
data1Dict[row[0]] = data1Dict.setdefault(row[0], []) + [row]
data2Dict = {}
for row in data2:
data2Dict[row[0]] = data2Dict.setdefault(row[0], []) + [row[1:]]
import os, sys, glob
import utilities
symbolsFilePath = sys.argv[1]
entrezGenesSymbolsFilePath = sys.argv[2]
entrezGenesSynonymsFilePath = sys.argv[3]
outFilePath = sys.argv[4]
symbols = utilities.readVectorFromFile(symbolsFilePath)
entrezGenesSymbolsData = utilities.readMatrixFromFile(entrezGenesSymbolsFilePath)
entrezGenesSymbolsDict = {}
for row in entrezGenesSymbolsData:
entrezGenesSymbolsDict[row[1]] = row[0]
entrezGenesSynonymsData = utilities.readMatrixFromFile(entrezGenesSynonymsFilePath)
entrezGenesSynonymsDict = {}
for row in entrezGenesSynonymsData:
for synonym in row[1].split("|"):
entrezGenesSynonymsDict[synonym] = entrezGenesSynonymsDict.setdefault(synonym, []) + [row[0]]
outFile = open(outFilePath, 'w')
for symbol in symbols:
if entrezGenesSymbolsDict.has_key(symbol):
entrezID = entrezGenesSymbolsDict[symbol]
else:
if entrezGenesSynonymsDict.has_key(symbol):
entrezIDs = entrezGenesSynonymsDict[symbol]
if len(entrezIDs) == 1:
entrezID = entrezIDs[0]
import os, sys, glob
import utilities
pathwaysFilePath = sys.argv[1]
genePathwayFilePath = sys.argv[2]
geneEntrezFilePath = sys.argv[3]
outFilePathTemplate = sys.argv[4] #KEGG_{PATHWAY_NAME}.gene.ids.txt
pathwaysData = utilities.readMatrixFromFile(pathwaysFilePath)
pathwaysData = [row for row in pathwaysData if not row[0].startswith("#")]
pathwaysDict = {}
for row in pathwaysData:
pathwaysDict[row[0]] = row[1].upper().replace(" - ", "_").replace(", ", "_").replace(" / ", "_").replace("-", "_").replace(" ", "_").replace("/", "_").replace("(", "").replace(")", "").replace(",", "_").replace("'", "")
genePathwayData = utilities.readMatrixFromFile(genePathwayFilePath)
genePathwayDict = {}
for row in genePathwayData:
gene = row[0]
for pathway in row[1].split(" "):
genePathwayDict[pathway] = genePathwayDict.setdefault(pathway, []) + [gene]
geneEntrezData = utilities.readMatrixFromFile(geneEntrezFilePath)
geneEntrezDict = {}
for row in geneEntrezData:
geneEntrezDict[row[0].replace("hsa:", "")] = row[1].replace("ncbi-geneid:", "")
for keggPathwayID in pathwaysDict.keys():
if not genePathwayDict.has_key(keggPathwayID):
continue
keggGeneIDs = genePathwayDict[keggPathwayID]
inFilePath = sys.argv[1]
classFilePath = sys.argv[2]
ignorePatientID = sys.argv[3]
includeIDs = sys.argv[4] == "True"
outFilePath = sys.argv[5]
patientClassDict = {}
for line in file(classFilePath):
if line.startswith("#"):
continue
lineItems = line.rstrip().split("\t")
patientClassDict[lineItems[0]] = lineItems[1]
if os.path.exists(inFilePath):
data = utilities.transposeMatrix(utilities.readMatrixFromFile(inFilePath))
features = data.pop(0)
features.pop(0)
else:
data = [[patientID] for patientID in patientClassDict.keys()]
features = []
outFile = open(outFilePath, "w")
outFile.write("@relation data\n\n")
if includeIDs:
outFile.write("@attribute id string\n")
for feature in features:
outFile.write("@attribute %s numeric\n" % feature.replace("'", "prime"))
import os, sys, glob, math
import utilities
from TransformFunctions import *
# See http://fluxcapacitor.wikidot.com/forum/t-333476
mappedReadsFilePath = sys.argv[1]
metaFilePath = sys.argv[2]
outFilePath = sys.argv[3]
mappedReads = utilities.readMatrixFromFile(mappedReadsFilePath)
READ_NR = math.fsum([float(x[1]) for x in mappedReads])
metaDict = {}
for metaRow in utilities.readMatrixFromFile(metaFilePath):
metaDict[metaRow[0]] = metaRow[4]
outData = []
for mappedRead in mappedReads:
id = mappedRead[0]
if id not in metaDict:
continue
reads = float(mappedRead[1])
length = float(metaDict[id])
rpkm = (reads * 1000000000) / (length * READ_NR)
outData.append((id, "%.9f" % rpkm))
import utilities
from VariantUtilities import *
inMetaFilePath = sys.argv[1]
genomeDirPath = sys.argv[2]
outFilePath = sys.argv[3]
def getChromosomeSequence(filePath):
sequence = ""
for line in file(filePath):
if not line.startswith(">"):
sequence += line.rstrip().upper()
return sequence
outData = []
inMeta = utilities.readMatrixFromFile(inMetaFilePath)
chromosomes = sorted(list(set([parseChromosome(x[1]) for x in inMeta])))
for chromosome in chromosomes:
print "Processing %s" % chromosome
faFilePath = genomeDirPath + "/" + chromosome + ".fa"
if not os.path.exists(faFilePath):
faFilePath = genomeDirPath + "/" + chromosome.replace("chr", "") + ".fa"
if not os.path.exists(faFilePath):
print "Ignoring %s because no chromosome file exists" % chromosome
continue
inMetaChromosome = [x for x in inMeta if x[1] == parseChromosome(chromosome)]
inFilePath = sys.argv[1]
classFilePath = sys.argv[2]
ignorePatientID = sys.argv[3]
includeIDs = sys.argv[4] == "True"
outFilePath = sys.argv[5]
patientClassDict = {}
for line in file(classFilePath):
if line.startswith("#"):
continue
lineItems = line.rstrip().split("\t")
patientClassDict[lineItems[0]] = lineItems[1]
if os.path.exists(inFilePath):
data = utilities.transposeMatrix(utilities.readMatrixFromFile(inFilePath))
features = data.pop(0)
features.pop(0)
else:
data = [[patientID] for patientID in patientClassDict.keys()]
features = []
outFile = open(outFilePath, 'w')
outFile.write("@relation data\n\n")
if includeIDs:
outFile.write("@attribute id string\n")
for feature in features:
outFile.write("@attribute %s numeric\n" % feature.replace("'", "prime"))
import os, sys, glob
import utilities
def pearson(x, y):
return utilities.calculatePearsonCoefficient(x, y)
def spearman(x, y):
return utilities.calculateSpearmanCoefficient(x, y)
matrix1FilePath = sys.argv[1]
matrix2FilePath = sys.argv[2]
byRow = sys.argv[3] == "True"
compareFunction = getattr(sys.modules[__name__], sys.argv[4])
outFilePath = sys.argv[5]
matrix1 = utilities.readMatrixFromFile(matrix1FilePath)
matrix2 = utilities.readMatrixFromFile(matrix2FilePath)
colNames = matrix1.pop(0)
matrix2.pop(0)
if byRow:
print "byRow Not yet implemented"
exit()
else:
results = []
for colIndex in range(1, len(matrix1[0])):
values1 = [float(row[colIndex]) for row in matrix1]
values2 = [float(row[colIndex]) for row in matrix2]
summarizeFunction = getattr(sys.modules[__name__], sys.argv[7])
outlierSamplesFilePath = sys.argv[8]
outFilePath = sys.argv[9]
outlierSamples = []
if os.path.exists(outlierSamplesFilePath):
outlierSamples = utilities.readVectorFromFile(outlierSamplesFilePath)
if patientID in outlierSamples:
print "%s is listed as an outlier, so it won't be summarized" % patientID
sys.exit(0)
print "Get data probes"
dataProbes = set([line.rstrip().split("\t")[0] for line in file(inFilePath)])
keyProbes = utilities.readMatrixFromFile(keyProbeFilePath)
keyProbes = [x for x in keyProbes if len(list(set(x[1].split(",")) & dataProbes)) > 0]
keyProbeDict = {}
for keyProbesRow in keyProbes:
keyProbeDict[keyProbesRow[0]] = keyProbeDict.setdefault(keyProbesRow[0], []) + keyProbesRow[1].split(",")
if os.path.exists(probeFilePath):
print "Keeping only specified probes"
keepProbes = set(utilities.readVectorFromFile(probeFilePath))
for key in keyProbeDict.keys():
keyProbeDict[key] = list(set(keyProbeDict[key]) & keepProbes)
else:
keepProbes = list(dataProbes)
import os, sys, glob, shutil
import utilities
## The input file should contain samples as columns and variables as rows
inFilePath = sys.argv[1]
classesFilePath = sys.argv[2]
outGctFilePath = sys.argv[3]
outClsFilePath = sys.argv[4]
data = utilities.readMatrixFromFile(inFilePath)
samples = data.pop(0)
if len(samples) == len(data[0]):
samples.pop(0)
classesDict = {}
for row in utilities.readMatrixFromFile(classesFilePath):
if row[0] in samples:
classesDict[row[0]] = row[1]
uniqueClasses = sorted(list(set(classesDict.values())))
variables = [x[0] for x in data]
outGctFile = open(outGctFilePath, 'w')
outGctFile.write("#1.2\n")
outGctFile.write("%i\t%i\n" % (len(variables), len(classesDict)))
outGctFile.write("NAME\tDescription\t")
outGctFile.write("\t".join([sample for sample in samples if classesDict.has_key(sample)]) + "\n")
for row in data:
outGctFile.write("%s\t%s\t" % (row[0], row[0]))