def CF_export(args):
try:
h5file_in_fn = str(args.input)
h5file_in = openFile(h5file_in_fn, mode='r')
except IOError as e:
print '[ERROR] Cannot open CoNIFER input file for reading: ', h5file_in_fn
sys.exit(0)
# read probes
probes = {}
for probes_chr in h5file_in.root.probes:
probes[probes_chr.title] = probes_chr.read()
if args.sample == 'all':
all_samples = list(
h5file_in.root.samples.samples.read(field="sampleID"))
out_path = os.path.abspath(args.output)
print "[INIT] Preparing to export all samples (%d samples) to %s" % (
len(all_samples), out_path)
for sample in all_samples:
try:
outfile_fn = out_path + "/" + sample + ".bed"
outfile_f = open(outfile_fn, 'w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', outfile_fn
sys.exit(0)
print "[RUNNING] Exporting %s" % sample
cf.export_sample(h5file_in, sample, probes, outfile_f)
outfile_f.close()
elif len(args.sample) == 1:
out_path = os.path.abspath(args.output)
sample = args.sample[0]
print "[INIT] Preparing to export sampleID %s to %s" % (args.sample[0],
out_path)
try:
if os.path.isdir(out_path):
outfile_fn = out_path + "/" + sample + ".bed"
else:
outfile_fn = out_path
outfile_f = open(outfile_fn, 'w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', outfile_fn
sys.exit(0)
print "[RUNNING] Exporting %s to %s" % (sample, outfile_fn)
cf.export_sample(h5file_in, sample, probes, outfile_f)
outfile_f.close()
else:
out_path = os.path.abspath(args.output)
print "[INIT] Preparing to export %d samples to %s" % (len(
args.sample), out_path)
for sample in args.sample:
try:
if os.path.isdir(out_path):
outfile_fn = out_path + "/" + sample + ".bed"
else:
outfile_fn = out_path
outfile_f = open(outfile_fn, 'w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', outfile_fn
sys.exit(0)
print "[RUNNING] Exporting %s to %s" % (sample, outfile_fn)
cf.export_sample(h5file_in, sample, probes, outfile_f)
outfile_f.close()
sys.exit(0)
def CF_export(args):
try:
h5file_in_fn = str(args.input)
h5file_in = openFile(h5file_in_fn, mode='r')
except IOError as e:
print '[ERROR] Cannot open CoNIFER input file for reading: ', h5file_in_fn
sys.exit(0)
# read probes
probes = {}
for probes_chr in h5file_in.root.probes:
probes[probes_chr.title] = probes_chr.read()
if args.sample =='all':
all_samples = list(h5file_in.root.samples.samples.read(field="sampleID"))
out_path = os.path.abspath(args.output)
print "[INIT] Preparing to export all samples (%d samples) to %s" % (len(all_samples), out_path)
for sample in all_samples:
try:
outfile_fn = out_path + "/" + sample + ".bed"
outfile_f = open(outfile_fn,'w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', outfile_fn
sys.exit(0)
print "[RUNNING] Exporting %s" % sample
cf.export_sample(h5file_in,sample,probes,outfile_f)
outfile_f.close()
elif len(args.sample) == 1:
out_path = os.path.abspath(args.output)
sample = args.sample[0]
print "[INIT] Preparing to export sampleID %s to %s" % (args.sample[0], out_path)
try:
if os.path.isdir(out_path):
outfile_fn = out_path + "/" + sample + ".bed"
else:
outfile_fn = out_path
outfile_f = open(outfile_fn,'w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', outfile_fn
sys.exit(0)
print "[RUNNING] Exporting %s to %s" % (sample, outfile_fn)
cf.export_sample(h5file_in,sample,probes,outfile_f)
outfile_f.close()
else:
out_path = os.path.abspath(args.output)
print "[INIT] Preparing to export %d samples to %s" % (len(args.sample), out_path)
for sample in args.sample:
try:
if os.path.isdir(out_path):
outfile_fn = out_path + "/" + sample + ".bed"
else:
outfile_fn = out_path
outfile_f = open(outfile_fn,'w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', outfile_fn
sys.exit(0)
print "[RUNNING] Exporting %s to %s" % (sample, outfile_fn)
cf.export_sample(h5file_in,sample,probes,outfile_f)
outfile_f.close()
sys.exit(0)