def readOptSm(argv, outputdir, selectodir, regionfile, genomefile, motiffile, exclude, prefix):
try:
opts, args = getopt.getopt(argv, "hf:g:m:o:", ["help", "name=", "excl="]) # List of all short and long options possible
except getopt.GetoptError:
usageSm()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"): # Print usage message
usageSm()
sys.exit(0)
elif opt == '-f': # For region bed file
checkBed(arg)
regionfile = arg
elif opt == '-g': # For genome fasta file
checkFasta(arg)
genomefile = arg
elif opt == '-o': # Output directory is specified
if not checkPath(arg):
print "Error, the specified path '"+arg+"' does not exists"
sys.exit(1)
outputdir = arg
selectodir = 'true'
elif opt == '--name': # Prefix to give to output file
prefix = arg
elif opt == '-m': # motif file to use for motif scanning
checkMotif(arg)
motiffile = arg
elif opt == '--excl': # genomic region to exclude when genrating backgrund files
checkExcl(arg)
exclude = arg
return outputdir, selectodir, regionfile, genomefile, motiffile, exclude, prefix
def readOptAp(argv, outputdir, selectodir, peakfile, annofile, peakcaller, prefix, graph):
try:
opts, args = getopt.getopt(argv, "hf:a:o:", ["help", "plot", "name="]) # List of all short and long options possible
except getopt.GetoptError:
usageAp()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"): # Print usage message
usageAp()
sys.exit(0)
elif opt == '-f': # For replicate 1 file
checkFile(arg)
peakfile = arg
elif opt == '-a': # For replicate 2 file
checkBed(arg)
annofile = arg
elif opt == '-o': # Output directory is specified
if not checkPath(arg):
print "Error, the specified path '"+arg+"' does not exists"
sys.exit(1)
outputdir = arg
selectodir = 'true'
elif opt == '--name': # Prefix to give to output file
prefix = arg
elif opt == '--plot':
graph = 'ON'
return outputdir, selectodir, peakfile, annofile, peakcaller, prefix, graph
def readOptMd(argv, outputdir, selectodir, regionfile, genomefile, database, scan, prefix):
try:
opts, args = getopt.getopt(argv, "hf:g:o:", ["help", "name=", "db="]) # List of all short and long options possible
except getopt.GetoptError:
usageMd()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"): # Print usage message
usageMd()
sys.exit(0)
elif opt == '-f': # For region bed file
checkBed(arg)
regionfile = arg
elif opt == '-g': # For genome fasta file
checkFasta(arg)
genomefile = arg
elif opt == '-o': # Output directory is specified
if not checkPath(arg):
print "Error, the specified path '"+arg+"' does not exists"
sys.exit(1)
outputdir = arg
selectodir = 'true'
elif opt == '--name': # Prefix to give to output file
prefix = arg
elif opt == '--db': # database to use for motif discovery
checkDataBase(arg)
scan = 'ON'
database = arg
return outputdir, selectodir, regionfile, genomefile, database, scan, prefix
def createOdir(
directory
): # Create an output directory in the current directory when no output directory is given
if checkPath(directory):
return
else:
os.mkdir(directory)
def readOptCa(argv, outputdir, selectodir, filterqual, unmapped, filtercoord, indexGenome, rmvdup, sorting, indexBam, coordinatefile, prefix, genome, minqual, fastqfile, fastqfile1, fastqfile2, seq):
try:
opts, args = getopt.getopt(argv, "hf:1:2:g:o:q:FL:", ["help", "index", "rmdup", "sort", "bamIndex", "name="]) # List of all short and long options possible
except getopt.GetoptError:
usageCa()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"): # Print usage message
usageCa()
sys.exit(0)
elif opt == '-f': # Means that just one SE fastq file is given
checkFastq(arg)
fastqfile = arg
seq = 'SE'
elif opt == '-1': # Means that R1 PE fastq file is given
checkFastq(arg)
fastqfile1 = arg
seq = 'PE'
elif opt == '-2': # Means that R2 PE fastq file is given
checkFastq(arg)
fastqfile2 = arg
elif opt == '-g': # genome prefix is given
checkGenome(arg)
genome = arg
elif opt == '-o': # Output directory is specified
if not checkPath(arg):
print "Error, the specified path '"+arg+"' does not exists"
sys.exit(1)
outputdir = arg
selectodir = 'true'
elif opt == '-q': # Filter out reads with low quality
minqual = arg # quality threshold
filterqual = 'ON'
elif opt == '-F': # Filter out unmapped reads
unmapped = 'ON'
elif opt == '-L': # Filter out reads in specific regions (blacklist)
checkFile(arg)
coordinatefile = arg # file name of blacklist regions
filtercoord = 'ON'
elif opt == '--index': # Indexing genome before alignment
indexGenome = 'ON'
elif opt == '--rmdup': # Filter out PCR duplicates and non uniquely mappable reads
rmvdup = 'ON'
elif opt == '--sort': # Sorting final bam file
sorting = 'ON'
elif opt == '--bamIndex': # Indexing final bam file
indexBam = 'ON'
elif opt == '--name': # Prefix to give to output file
prefix = arg
return outputdir, selectodir, filterqual, unmapped, filtercoord, indexGenome, rmvdup, sorting, indexBam, coordinatefile, prefix, genome, minqual, fastqfile, fastqfile1, fastqfile2, seq
def readOptCp(argv, outputdir, selectodir, rep1, rep2, ctrl1, ctrl2, ctrlsup, idr, idrthresh, finalsets, plot, prefix):
try:
opts, args = getopt.getopt(argv, "h1:2:o:", ["help", "c1=", "c2=", "idr=", "sets", "no-plots", "name="]) # List of all short and long options possible
except getopt.GetoptError:
usageCp()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"): # Print usage message
usageCp()
sys.exit(0)
elif opt == '-1': # For replicate 1 file
checkBam(arg)
rep1 = arg
elif opt == '-2': # For replicate 2 file
checkBam(arg)
rep2 = arg
elif opt == '-o': # Output directory is specified
if not checkPath(arg):
print "Error, the specified path '"+arg+"' does not exists"
sys.exit(1)
outputdir = arg
selectodir = 'true'
elif opt == '--c1': # For control file
checkBam(arg)
ctrl1 = arg
elif opt == '--c2': # For supplemental control file
checkBam(arg)
ctrl2 = arg
ctrlsup = 'true'
elif opt == '--idr': # Perform IDR analysis
idr = 'ON'
idrthresh = arg
elif opt == '--sets': # Create final peak sets
finalsets = 'ON'
elif opt == '--no-plots': # Create final peak sets
plot = 'OFF'
elif opt == '--name': # Prefix to give to output file
prefix = arg
return outputdir, selectodir, rep1, rep2, ctrl1, ctrl2, ctrlsup, idr, idrthresh, finalsets, plot, prefix
def readOptTq(argv, outputdir, selectodir, fastqfile1, fastqfile2, fastqfile, seq1, seq2, lib):
try:
opts, args = getopt.getopt(argv, "hf:1:2:o:", ["help", "lib=", "adapt="]) # List of all short and long options possible
except getopt.GetoptError:
usageTq()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"): # Print usage message
usageTq()
sys.exit(0)
elif opt == '-f': # for SE fastq file
checkFastq(arg)
fastqfile = arg
seq1 = 'SE'
elif opt == '-1': # For R1 fastq file
checkFastq(arg)
fastqfile1 = arg
seq1 = 'PE'
elif opt == '-2': # For R2 fastq file
checkFastq(arg)
fastqfile2 = arg
elif opt == '-o': # Output directory is specified
if not checkPath(arg):
print "Error, the specified path '"+arg+"' does not exists"
sys.exit(1)
outputdir = arg
selectodir = 'true'
elif opt == '--lib': # For control file
checkLib(arg)
lib = arg
elif opt == '--adapt': # For supplemental control file
if arg != 'SE' and arg != 'PE':
print "Error, wrong parameter used for --adapt options, must be 'SE' or 'PE'"
sys.exit(1)
seq2 = arg
return outputdir, selectodir, fastqfile1, fastqfile2, fastqfile, seq1, seq2, lib
def readOptCpnr(argv, outputdir, selectodir, bamfile, ctrlfile, thresh, pvalue, qvalue, qc, prefix , spp):
try:
opts, args = getopt.getopt(argv, "hf:c:o:pq", ["help", "thresh=", "spp-qual", "name=", "spp-call"]) # List of all short and long options possible
except getopt.GetoptError:
usageCpnr()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"): # Print usage message
usageCpnr()
sys.exit(0)
elif opt == '-f': # For replicate 1 file
checkBam(arg)
bamfile = arg
elif opt == '-c': # For replicate 2 file
checkBam(arg)
ctrlfile = arg
elif opt == '-o': # Output directory is specified
if not checkPath(arg):
print "Error, the specified path '"+arg+"' does not exists"
sys.exit(1)
outputdir = arg
selectodir = 'true'
elif opt == '-p': # p-value threshold
pvalue = 'ON'
elif opt == '-q': # q-value threshold
qvalue = 'ON'
pvalue = 'OFF'
elif opt == '--thresh': # Perform IDR analysis
thresh = arg
elif opt == '--spp-qual': # Control read quality with cross correlation before peak calling
qc = 'ON'
elif opt == '--spp-call': # Call peak on alternative way
spp = 'ON'
elif opt == '--name': # Prefix to give to output file
prefix = arg
return outputdir, selectodir, bamfile, ctrlfile, thresh, pvalue, qvalue, qc, prefix, spp
def createOdir(directory): # Create an output directory in the current directory when no output directory is given if checkPath(directory): return else: os.mkdir(directory)