def CF_call(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)
try:
callfile_fn = str(args.output)
callfile_f = open(callfile_fn, mode='w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', callfile_fn
sys.exit(0)
chrs_to_process = []
for chr in h5file_in.root:
if chr._v_title not in ('probes', 'samples'):
chrs_to_process.append(chr._v_title.replace("chr", ""))
h5file_in.close()
print '[INIT] Initializing caller at threshold = %f' % (args.threshold)
r = cf.rpkm_reader(h5file_in_fn)
all_calls = []
for chr in chrs_to_process:
print '[RUNNING] Now processing chr%s' % chr
data = r.getExonValuesByRegion(chr)
#raw_data = copy.copy(data)
_ = data.smooth()
mean = np.mean(data.rpkm, axis=1)
sd = np.std(data.rpkm, axis=1)
for sample in r.getSampleList():
sample_data = data.getSample([sample]).flatten()
#sample_raw_data = raw_data.getSample([sample]).flatten()
dup_mask = sample_data >= args.threshold
del_mask = sample_data <= -1 * args.threshold
dup_bkpoints = cf.getbkpoints(
dup_mask
) #returns exon coordinates for this chromosome (numpy array coords)
del_bkpoints = cf.getbkpoints(del_mask)
dups = []
for start, stop in dup_bkpoints:
try:
new_start = np.max(
np.where(sample_data[:start] < (mean[:start] +
3 * sd[:start])))
except ValueError:
new_start = 0
try:
new_stop = stop + np.min(
np.where(sample_data[stop:] <
(mean[stop:] + 3 * sd[stop:])))
except ValueError:
new_stop = data.shape[1] - 1
dups.append({
"sampleID": sample,
"chromosome": cf.chrInt2Str(chr),
"start": data.exons[new_start]["start"],
"stop": data.exons[new_stop]["stop"],
"state": "dup"
})
dels = []
for start, stop in del_bkpoints:
try:
new_start = np.max(
np.where(sample_data[:start] > (-1 * mean[:start] -
3 * sd[:start])))
except ValueError:
new_start = 0
try:
new_stop = stop + np.min(
np.where(sample_data[stop:] >
(-1 * mean[stop:] - 3 * sd[stop:])))
except ValueError:
new_stop = data.shape[1] - 1
dels.append({
"sampleID": sample,
"chromosome": cf.chrInt2Str(chr),
"start": data.exons[new_start]["start"],
"stop": data.exons[new_stop]["stop"],
"state": "del"
})
dels = cf.mergeCalls(dels) #merges overlapping calls
dups = cf.mergeCalls(dups)
#print sampleID, len(dels), len(dups)
all_calls.extend(list(dels))
all_calls.extend(list(dups))
# print calls to file
header = ['sampleID', 'chromosome', 'start', 'stop', 'state']
callfile_f.write('\t'.join(header) + "\n")
for call in all_calls:
print "%s\t%s\t%d\t%d\t%s" % (call["sampleID"], call["chromosome"],
call["start"], call["stop"],
call["state"])
callfile_f.write("%s\t%s\t%d\t%d\t%s\n" %
(call["sampleID"], call["chromosome"], call["start"],
call["stop"], call["state"]))
sys.exit(0)
def CF_call(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)
try:
callfile_fn = str(args.output)
callfile_f = open(callfile_fn, mode='w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', callfile_fn
sys.exit(0)
chrs_to_process = []
for chr in h5file_in.root:
if chr._v_title not in ('probes','samples'):
chrs_to_process.append(chr._v_title.replace("chr",""))
h5file_in.close()
print '[INIT] Initializing caller at threshold = %f' % (args.threshold)
r = cf.rpkm_reader(h5file_in_fn)
all_calls = []
for chr in chrs_to_process:
print '[RUNNING] Now processing chr%s' % chr
data = r.getExonValuesByRegion(chr)
#raw_data = copy.copy(data)
_ = data.smooth()
mean= np.mean(data.rpkm,axis=1)
sd = np.std(data.rpkm,axis=1)
for sample in r.getSampleList():
sample_data = data.getSample([sample]).flatten()
#sample_raw_data = raw_data.getSample([sample]).flatten()
dup_mask = sample_data >= args.threshold
del_mask = sample_data <= -1*args.threshold
dup_bkpoints = cf.getbkpoints(dup_mask) #returns exon coordinates for this chromosome (numpy array coords)
del_bkpoints = cf.getbkpoints(del_mask)
dups = []
for start,stop in dup_bkpoints:
try: new_start = np.max(np.where(sample_data[:start] < (mean[:start] + 3*sd[:start])))
except ValueError: new_start = 0
try: new_stop = stop + np.min(np.where(sample_data[stop:] < (mean[stop:] + 3*sd[stop:])))
except ValueError: new_stop = data.shape[1]-1
dups.append({"sampleID":sample,"chromosome": cf.chrInt2Str(chr), "start":data.exons[new_start]["start"], "stop": data.exons[new_stop]["stop"], "state": "dup"})
dels = []
for start,stop in del_bkpoints:
try: new_start = np.max(np.where(sample_data[:start] > (-1*mean[:start] - 3*sd[:start])))
except ValueError: new_start = 0
try: new_stop = stop + np.min(np.where(sample_data[stop:] > (-1*mean[stop:] - 3*sd[stop:])))
except ValueError: new_stop = data.shape[1]-1
dels.append({"sampleID":sample,"chromosome": cf.chrInt2Str(chr), "start":data.exons[new_start]["start"], "stop": data.exons[new_stop]["stop"], "state": "del"})
dels = cf.mergeCalls(dels) #merges overlapping calls
dups = cf.mergeCalls(dups)
#print sampleID, len(dels), len(dups)
all_calls.extend(list(dels))
all_calls.extend(list(dups))
# print calls to file
header = ['sampleID','chromosome','start','stop','state']
callfile_f.write('\t'.join(header) + "\n")
for call in all_calls:
print "%s\t%s\t%d\t%d\t%s" % (call["sampleID"], call["chromosome"], call["start"], call["stop"], call["state"])
callfile_f.write("%s\t%s\t%d\t%d\t%s\n" % (call["sampleID"], call["chromosome"], call["start"], call["stop"], call["state"]))
sys.exit(0)