class BedAnno(object):
def __init__(self, reference, trans=None, genes=None):
self.refdb = os.path.join(database_dir, "transdb",
"ncbi_anno_rel104.dbref.db")
reference = os.path.abspath(reference)
self.HGVS = HGVS(self.refdb, reference, trans, genes)
self._dbhandles = list()
dbtitle = defaultdict(float)
for f in glob(os.path.join(database_dir, "*", "*.bedanno.config")):
dbs = AnnoVar(os.path.abspath(f))
t = "\t".join([str(i) for i in sorted(dbs.search_value.values())])
dbtitle[t] = dbs.order
self._dbhandles.append(dbs)
self.dbtitle = "\t".join(
[j for j in sorted(dbtitle.keys(), key=lambda x: dbtitle[x])])
def __del__(self):
self.HGVS.__del__()
for dbs in self._dbhandles:
dbs.__del__()
def dbanno(self, variation):
dbinfo = defaultdict(set)
for dbs in self._dbhandles:
try:
infos = dbs.fetch(**variation.__dict__)
for info in infos:
for k, v in info.__dict__.iteritems():
if v != ".":
dbinfo[k].add(v)
except Exception:
continue
return dbinfo
def bedanno(self, bedfile, fileout=sys.stdout):
if not (bedfile and os.path.isfile(bedfile)):
raise IOError("Fail to load file: %s" % bedfile)
regions = smart_open(bedfile).readlines()
f_out = smart_open(fileout, 'w')
titles = "Transcript\tgeneSym\tgeneSym\tcHGVS\tProtein\tStand\tExonRegions"
for line in regions:
rows = line.strip().split("\t")
if len(rows) < 3:
f_out.write(line)
try:
chrom = str(rows[0])
start = int(rows[1])
stop = int(rows[2])
except ValueError:
if len(self.dbtitle):
f_out.write("\t".join(rows) +
'\t'.join([titles, self.dbtitle]) + '\n')
else:
f_out.write("\t".join(rows) + '\t' + titles + '\n')
continue
anno_m = self.HGVS.annobed(chrom, start, stop)
for anno in anno_m:
dbinfo = self.dbanno(anno)
rows[0] = str(anno.Chrom)
rows[1] = str(anno.Start)
rows[2] = str(anno.Stop)
trans = str(anno.Transcript)
gene = str(anno.geneSym)
chgvs = str(anno.cHgvs)
protein = str(anno.Protein)
stand = str(anno.Stand)
exons = str(anno.ExonRegions)
anno_message = [
str(i) for i in rows +
[trans, gene, chgvs, protein, stand, exons]
]
for i in self.dbtitle.split("\t"):
if i in dbinfo:
anno_message.append(";".join(dbinfo[i]))
else:
anno_message.append(".")
f_out.write("\t".join(anno_message) + '\n')
f_out.close()
class BedAnno(object):
def __init__(self, reference, trans=None, genes=None):
self.refdb = os.path.join(database_dir, "transdb", "ncbi_anno_rel104.dbref.db")
reference = os.path.abspath(reference)
self.HGVS = HGVS(self.refdb, reference, trans, genes)
self._dbhandles = list()
dbtitle = defaultdict(float)
for f in glob(os.path.join(database_dir, "*", "*.bedanno.config")):
dbs = AnnoVar(os.path.abspath(f))
t = "\t".join([str(i) for i in sorted(dbs.search_value.values())])
dbtitle[t] = dbs.order
self._dbhandles.append(dbs)
self.dbtitle = "\t".join([j for j in sorted(dbtitle.keys(), key=lambda x: dbtitle[x])])
def __del__(self):
self.HGVS.__del__()
for dbs in self._dbhandles:
dbs.__del__()
def dbanno(self, variation):
dbinfo = defaultdict(set)
for dbs in self._dbhandles:
try:
infos = dbs.fetch(**variation.__dict__)
for info in infos:
for k, v in info.__dict__.iteritems():
if v != ".":
dbinfo[k].add(v)
except Exception:
continue
return dbinfo
def bedanno(self, bedfile, fileout=sys.stdout):
if not (bedfile and os.path.isfile(bedfile)):
raise IOError("Fail to load file: %s" % bedfile)
regions = smart_open(bedfile).readlines()
f_out = smart_open(fileout, 'w')
titles = "Transcript\tgeneSym\tgeneSym\tcHGVS\tProtein\tStand\tExonRegions"
for line in regions:
rows = line.strip().split("\t")
if len(rows) < 3:
f_out.write(line)
try:
chrom = str(rows[0])
start = int(rows[1])
stop = int(rows[2])
except ValueError:
if len(self.dbtitle):
f_out.write("\t".join(rows) + '\t'.join([titles, self.dbtitle]) + '\n')
else:
f_out.write("\t".join(rows) + '\t' + titles + '\n')
continue
anno_m = self.HGVS.annobed(chrom, start, stop)
for anno in anno_m:
dbinfo = self.dbanno(anno)
rows[0] = str(anno.Chrom)
rows[1] = str(anno.Start)
rows[2] = str(anno.Stop)
trans = str(anno.Transcript)
gene = str(anno.geneSym)
chgvs = str(anno.cHgvs)
protein = str(anno.Protein)
stand = str(anno.Stand)
exons = str(anno.ExonRegions)
anno_message = [str(i) for i in rows + [trans, gene, chgvs, protein, stand, exons]]
for i in self.dbtitle.split("\t"):
if i in dbinfo:
anno_message.append(";".join(dbinfo[i]))
else:
anno_message.append(".")
f_out.write("\t".join(anno_message) + '\n')
f_out.close()
