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 parse(self, outdir=os.getcwd(), kickout_function=None, follow_function=None):
logger.info("General VCF Phrasing begin !!!")
self.vcf.parse_metainfo()
titles = ["Chrom", "Start", "Stop", "Refer", "Call", "Zygosity", "VarType", "Filter", "ADepth", "ARatio",
"PL", "NeighborGID", "PhasedGID", "MutationName", "GeneSym", "EntrezGeneID", "Transcript",
"TransBioType", "cHGVS", "Protein", "pHGVS", "Strand", "PrimaryTag", "FunctionName", "Impact",
"ExInID", "cDNAPos", "AAPos", "CDSPos", "AnnoTag", "StandardMutation"]
annotation = namedtuple("Annotation", titles)
dbtitle = self.DBAnno.dbtitle.split("\t")
titles.extend(dbtitle)
kickouts = kickout_function.split(",") if kickout_function else list()
follows = follow_function.split(",") if follow_function else None
for name, samples in self.vcf.readlines.iteritems():
logger.info("Start to annotate sample %s" % name)
message_num = 0
result_out = list()
for messages in samples:
chrom = messages.Chrom
pos = int(messages.Pos)
gt = re.compile("(\d)[|/](\d)").match(messages.GT)
if not gt:
continue
message_num += 1
if message_num % 250 == 0:
logger.info("Complete " + str(message_num) + " articles")
l1, l2 = int(gt.group(1)), int(gt.group(2))
refer = messages.Ref
alter_1 = messages.Alter[l1 - 1] if l1 > 0 else refer
alter_2 = messages.Alter[l2 - 1] if l2 > 0 else refer
alter_out_set = set()
eff_info_dict = self.get_snpeff_info(messages.Info['ANN'])
try:
nb_id = messages.NB
except AttributeError:
nb_id = "."
try:
pb_id = messages.PB
except AttributeError:
pb_id = "."
filter_tag = messages.Filter
if l1 == l2:
zygosity = "hom-ref" if l1 == 0 else "hom-alt"
alter_out_set.add(alter_1)
else:
zygosity = "het-alt"
if l1 != 0:
alter_out_set.add(alter_1)
if l2 != 0:
alter_out_set.add(alter_2)
for alters in alter_out_set:
offset_s, offset_e, nor_refer, nor_alter, vartype, close_anno = \
self.closet_anno(chrom, pos, refer, alters)
start = pos + offset_s
stop = pos + + offset_e
for info_rows in eff_info_dict[alters]:
if not len(info_rows):
info_rows = (".",) * 16
genesym, gene_id, trans, trans_bio, chgvs, protein_id, phgvs, strand, primary, \
functions, impact, exon_num, cdna_pos, aa_pos, cds_pos, anno_tag = info_rows
functions = re.sub("_variant", "", functions)
if (functions in kickouts) or (follows and functions not in follow_function):
continue
if chgvs != ".":
mutation_name = "{0}({1}): {2}".format(trans, genesym, chgvs)
mutation_name += " (%s)" % phgvs if phgvs != "." else ""
else:
mutation_name = "."
try:
alle_depth = int(messages.AD.split(",")[l2])
try:
base_depth = int(messages.DP)
alle_radio = round(float(alle_depth) / base_depth, 2)
except Exception:
alle_radio = "."
except Exception:
alle_depth = "."
alle_radio = "."
try:
phred = ",".join(messages.PL.split(",")[3 * (l2 - 1): 3 * l2])
except Exception:
phred = "."
varinfo = [chrom, start, stop, nor_refer, nor_alter, zygosity, vartype, filter_tag, alle_depth,
alle_radio, phred, nb_id, pb_id, mutation_name, genesym, gene_id, trans, trans_bio,
chgvs, protein_id, phgvs, strand, primary, functions, impact, exon_num, cdna_pos,
aa_pos, cds_pos, anno_tag, close_anno]
variation = annotation._make(varinfo)
dbinfo = self.DBAnno.dbanno(variation)
for i in dbtitle:
if i in dbinfo:
varinfo.append("|".join(dbinfo[i]))
else:
varinfo.append(".")
result_out.append(varinfo)
sample_out = os.path.join(outdir, "%s.anno.tsv" % name)
f_out = open(sample_out, "w")
f_out.write("#" + "\t".join(titles) + '\n')
for anno_message in sorted(result_out, key=lambda x: (_chrom_valued(x[0]), int(x[1]), int(x[2]))):
f_out.write("\t".join(map(str, anno_message)) + '\n')
f_out.close()
fileout = pysam.tabix_index(sample_out, seq_col=0, start_col=1, end_col=2, force=True)
logger.info(
"Sample {0} [{1}]: Annotation completed, total {2} articles !".format(name, fileout, message_num))
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)
