def graph(depthfile, messages, outdir=os.getcwd(), prefix="Test", uncoverthreshold=5):
depth = pysam.TabixFile(depthfile)
plot_data = defaultdict(list)
genes = str
trans = str
for exon_message in sorted(messages, key=lambda x: _exon_vaule(x[2])):
if len(exon_message) != 6:
continue
trans, genes, exon_name, refchrom, refstart, refend = exon_message
try:
chrom = str(refchrom)
if chrom.startswith("chrM"):
chrom = 'chrM_NC_012920.1'
start = int(refstart)
end = int(refend)
except Exception:
continue
if chrom not in depth.contigs:
continue
array = list()
for depth_m in depth.fetch(chrom, start - 1, end):
rows = depth_m.strip().split('\t')
if len(rows) < 3:
raise IOError("depth file format Error !")
d = rows[-1]
array.append(int(d))
if not len(array):
array = [0] * (end - start + 1)
depth_message = DescribeArray(array)
plot_data["averagedepth"].append(depth_message.average)
plot_data["mediandepth"].append(depth_message.median)
coverate = float(depth_message.get_frequece(uncoverthreshold).strip('%'))
plot_data["coverate"].append(coverate)
plot_data["x_axis"].append(exon_name)
depth.close()
plot(plot_data, outdir, prefix, genes, trans)
def depths(self, bed, prefix=None, read_filter='all', qual_threshold=15, count_threshold=None, uncover_threshold=5):
threshold_type = type(count_threshold)
if threshold_type is list or threshold_type is tuple:
count_threshold = set(count_threshold)
elif count_threshold is set:
pass
else:
count_threshold = {1, 4, 10, 20, 30, 100}
uncover_threshold = max(int(uncover_threshold), 1)
count_threshold.add(uncover_threshold)
count_threshold = sorted(count_threshold, key=int)
outdir, name = os.path.split(os.path.abspath(prefix)) if prefix else (os.getcwd(), 'Rhea_Chip')
depth = os.path.join(outdir, '%s.depth.tsv' % name)
bedstat = os.path.join(outdir, '%s.bed.stat' % name)
stats = os.path.join(outdir, '%s.stat' % name)
chromstat = os.path.join(outdir, '%s.chrom.stat' % name)
uncover = os.path.join(outdir, '%s.uncover.bed' % name)
_depth = smart_open(depth, 'w')
_bedstat = smart_open(bedstat, 'w')
_stats = smart_open(stats, 'w')
_chromstat = smart_open(chromstat, 'w')
# _depth.write("#Chrom\tPos\tRef\tCov_A\tCov_C\tCov_G\tCov_T\tDepth\tWinGC_%s\n" % str(gcwin))
_depth.write("#Chrom\tPos\tRef\tCov_A\tCov_C\tCov_G\tCov_T\tDepth\n")
_bedstat.write("#Chr\tStart\tStop\tAverage\tMedian\tMax\tMin\n")
_stats.write("##A Simple introduction about %s\n" % self.name)
_chromstat.write("#Chr\tAverage\tMedian\tMax\tMin\t")
_chromstat.write("\t".join(["Coverage (>=%sX)" % str(key) for key in count_threshold]) + '\n')
chroms = defaultdict(dict)
rangedict = defaultdict(int)
regiondict = defaultdict(int)
total_base = 0
region_num = 0
with smart_open(bed) as regions:
for region in regions:
rows = region.strip().split()
if len(rows) < 3:
continue
try:
chrom = rows[0]
start = max(int(rows[1]) - 1, 0)
stop = min(int(rows[2]) + 1, self.reference.get_reference_length(chrom))
except Exception:
continue
cov_a, cov_c, cov_g, cov_t = self._reader.count_coverage(chrom, start, stop, read_callback=read_filter,
quality_threshold=int(qual_threshold))
bases = self.reference.fetch(chrom, start, stop).upper()
reg = list()
chrom = "chr" + re.sub("^chr", "", chrom)
if chrom.startswith("chrM"):
chrom = 'chrM_NC_012920.1'
for n in xrange(start, stop):
offset = n - start
dep = [bases[offset], cov_a[offset], cov_c[offset], cov_g[offset], cov_t[offset]]
base_depth = sum(dep[1:])
dep.append(base_depth)
# gc_radio = round(self.count_gc(bases[offset:offset + 201]), 4)
# dep.append(gc_radio)
chroms[chrom][n] = dep
for num in count_threshold:
num = int(num)
if base_depth >= num:
rangedict[num] += 1
total_base += 1
reg.append(base_depth)
region_num += 1
array = DescribeArray(reg)
averages = str(round(array.average, 2))
mediandepth = str(round(array.median, 2))
maxdepth = str(round(array.max, 2))
mindepth = str(round(array.min, 2))
_bedstat.write("\t".join([chrom, rows[1], rows[2], averages, mediandepth, maxdepth, mindepth]) + '\n')
for num in count_threshold:
num = int(num)
if array.average >= num:
regiondict[num] += 1
uncover_range = list()
n_array = list()
for chrom in sorted(chroms.keys(), key=lambda x: _chrom_valued(x)):
dep = sorted(chroms[chrom].iteritems(), key=lambda x: int(x[0]))
array = list()
for p, d in dep:
_depth.write("\t".join([chrom, str(p), '\t'.join([str(i) for i in d])]) + '\n')
array.append(d)
n_array.append(d[5])
array = DescribeArray(array, col=5)
averages = str(round(array.average, 2))
mediandepth = str(round(array.median, 2))
maxdepth = str(round(array.max, 2))
mindepth = str(round(array.min, 2))
chromcover = [array.get_frequece(thre, col=5) for thre in count_threshold]
_chromstat.write("\t".join([chrom, averages, mediandepth, maxdepth, mindepth] + chromcover) + '\n')
if read_filter == 'all':
uncover_bases = [int(p) for p, d in dep if d[5] < uncover_threshold]
uncover_range.extend(formact_number_list_to_range(uncover_bases, tag=chrom))
if read_filter == 'all':
uncoverout = smart_open(uncover, 'w')
uncoverout.write("#Chr\tStart\tStop\n")
uncoverout.writelines(uncover_range)
uncoverout.close()
array = DescribeArray(n_array)
_stats.write("Average depth : %.2f\n" % array.average)
_stats.write("Median depth : %.2f\n" % array.median)
_stats.write("Max depth : %.2f\n" % array.max)
_stats.write("Min depth : %.2f\n" % array.min)
for number in count_threshold:
number = int(number)
_stats.write("Coverage (>={0:d}X) : {1:.2f}%\n".format(
number, (float(rangedict[number]) / total_base) * 100, 2))
for number in count_threshold:
number = int(number)
_stats.write("Region Coverage (>={0:d}X) : {1:.2f}%\n".format(
number, (float(regiondict[number]) / region_num) * 100, 2))
_depth.close()
_bedstat.close()
_stats.close()
_chromstat.close()
dep_f = CreatIndex(depth)
_ = dep_f.check_index(seq_col=0, start_col=1, end_col=1)
def depths(self,
bed,
prefix=None,
read_filter='all',
qual_threshold=15,
count_threshold=None,
uncover_threshold=5):
threshold_type = type(count_threshold)
if threshold_type is list or threshold_type is tuple:
count_threshold = set(count_threshold)
elif count_threshold is set:
pass
else:
count_threshold = {1, 4, 10, 20, 30, 100}
uncover_threshold = max(int(uncover_threshold), 1)
count_threshold.add(uncover_threshold)
count_threshold = sorted(count_threshold, key=int)
outdir, name = os.path.split(
os.path.abspath(prefix)) if prefix else (os.getcwd(), 'Rhea_Chip')
depth = os.path.join(outdir, '%s.depth.tsv' % name)
bedstat = os.path.join(outdir, '%s.bed.stat' % name)
stats = os.path.join(outdir, '%s.stat' % name)
chromstat = os.path.join(outdir, '%s.chrom.stat' % name)
uncover = os.path.join(outdir, '%s.uncover.bed' % name)
_depth = smart_open(depth, 'w')
_bedstat = smart_open(bedstat, 'w')
_stats = smart_open(stats, 'w')
_chromstat = smart_open(chromstat, 'w')
# _depth.write("#Chrom\tPos\tRef\tCov_A\tCov_C\tCov_G\tCov_T\tDepth\tWinGC_%s\n" % str(gcwin))
_depth.write("#Chrom\tPos\tRef\tCov_A\tCov_C\tCov_G\tCov_T\tDepth\n")
_bedstat.write("#Chr\tStart\tStop\tAverage\tMedian\tMax\tMin\n")
_stats.write("##A Simple introduction about %s\n" % self.name)
_chromstat.write("#Chr\tAverage\tMedian\tMax\tMin\t")
_chromstat.write("\t".join(
["Coverage (>=%sX)" % str(key) for key in count_threshold]) + '\n')
chroms = defaultdict(dict)
rangedict = defaultdict(int)
regiondict = defaultdict(int)
total_base = 0
region_num = 0
with smart_open(bed) as regions:
for region in regions:
rows = region.strip().split()
if len(rows) < 3:
continue
try:
chrom = rows[0]
start = max(int(rows[1]) - 1, 0)
stop = min(
int(rows[2]) + 1,
self.reference.get_reference_length(chrom))
except Exception:
continue
cov_a, cov_c, cov_g, cov_t = self._reader.count_coverage(
chrom,
start,
stop,
read_callback=read_filter,
quality_threshold=int(qual_threshold))
bases = self.reference.fetch(chrom, start, stop).upper()
reg = list()
chrom = "chr" + re.sub("^chr", "", chrom)
if chrom.startswith("chrM"):
chrom = 'chrM_NC_012920.1'
for n in xrange(start, stop):
offset = n - start
dep = [
bases[offset], cov_a[offset], cov_c[offset],
cov_g[offset], cov_t[offset]
]
base_depth = sum(dep[1:])
dep.append(base_depth)
# gc_radio = round(self.count_gc(bases[offset:offset + 201]), 4)
# dep.append(gc_radio)
chroms[chrom][n] = dep
for num in count_threshold:
num = int(num)
if base_depth >= num:
rangedict[num] += 1
total_base += 1
reg.append(base_depth)
region_num += 1
array = DescribeArray(reg)
averages = str(round(array.average, 2))
mediandepth = str(round(array.median, 2))
maxdepth = str(round(array.max, 2))
mindepth = str(round(array.min, 2))
_bedstat.write("\t".join([
chrom, rows[1], rows[2], averages, mediandepth, maxdepth,
mindepth
]) + '\n')
for num in count_threshold:
num = int(num)
if array.average >= num:
regiondict[num] += 1
uncover_range = list()
n_array = list()
for chrom in sorted(chroms.keys(), key=lambda x: _chrom_valued(x)):
dep = sorted(chroms[chrom].iteritems(), key=lambda x: int(x[0]))
array = list()
for p, d in dep:
_depth.write("\t".join(
[chrom, str(p), '\t'.join([str(i) for i in d])]) + '\n')
array.append(d)
n_array.append(d[5])
array = DescribeArray(array, col=5)
averages = str(round(array.average, 2))
mediandepth = str(round(array.median, 2))
maxdepth = str(round(array.max, 2))
mindepth = str(round(array.min, 2))
chromcover = [
array.get_frequece(thre, col=5) for thre in count_threshold
]
_chromstat.write(
"\t".join([chrom, averages, mediandepth, maxdepth, mindepth] +
chromcover) + '\n')
if read_filter == 'all':
uncover_bases = [
int(p) for p, d in dep if d[5] < uncover_threshold
]
uncover_range.extend(
formact_number_list_to_range(uncover_bases, tag=chrom))
if read_filter == 'all':
uncoverout = smart_open(uncover, 'w')
uncoverout.write("#Chr\tStart\tStop\n")
uncoverout.writelines(uncover_range)
uncoverout.close()
array = DescribeArray(n_array)
_stats.write("Average depth : %.2f\n" % array.average)
_stats.write("Median depth : %.2f\n" % array.median)
_stats.write("Max depth : %.2f\n" % array.max)
_stats.write("Min depth : %.2f\n" % array.min)
for number in count_threshold:
number = int(number)
_stats.write("Coverage (>={0:d}X) : {1:.2f}%\n".format(
number, (float(rangedict[number]) / total_base) * 100, 2))
for number in count_threshold:
number = int(number)
_stats.write("Region Coverage (>={0:d}X) : {1:.2f}%\n".format(
number, (float(regiondict[number]) / region_num) * 100, 2))
_depth.close()
_bedstat.close()
_stats.close()
_chromstat.close()
dep_f = CreatIndex(depth)
_ = dep_f.check_index(seq_col=0, start_col=1, end_col=1)