def snpinfo(infile,
outfile=None,
notfound='ignore',
genome='hg19',
dbsnpver="150",
inopts=None,
outopts=None,
snpcol=None,
cachedir=gettempdir()):
_inopts = Box(skip=0, comment='#', delimit='\t')
_inopts.update(inopts or {})
inopts = _inopts
_outopts = Box(delimit='\t',
headDelimit='\t',
headPrefix='',
headTransform=None,
head=True,
ftype='bed',
cnames='refUCSC, alleles, alleleFreqs, alleleFreqCount')
_outopts.update(outopts)
outopts = _outopts
cnames = alwaysList(outopts['cnames'])
reader = TsvReader(infile, **inopts)
if not reader.meta: reader.autoMeta()
snpcol = snpcol or reader.meta.keys()[0]
snps = list(set([r[snpcol] for r in reader]))
reader.rewind()
dbfile = path.join(cachedir, 'snpinfo_%s_%s.db' % (genome, dbsnpver))
schema = {
'chrom': 'text', # chr8
'chromStart': 'int', # 128700232L
'chromEnd': 'end', # 128700233L
'name': 'text primary key', # rs7005394
'score': 'real', # 0
'strand': 'text', # +
'refNCBI': 'text', # T
'refUCSC': 'text', # T
'observed': 'text', # C/T
'class': 'single', # single
'avHet': 'real', # 0.49
'avHetSE': 'real', # 0.02
'func': 'text', # set(['ncRNA'])
'submitterCount': 'int', # 20
'submitters':
'text', # 1000GENOMES,ABI,BCM-HGSC-SUB,BCM_SSAHASNP,BGI,BL ...
'alleleFreqCount': 'int', # 2
'alleles': 'text', # C,T,
'alleleNs': 'text', # 2634.000000,2374.000000,
'alleleFreqs': 'text', # 0.525958,0.474042,
}
cache = Cache(dbfile, 'snpinfo', schema, 'name')
dummies = {
'func':
dict(query=Cache.DUMMY['array']['query'],
find=Cache.DUMMY['array']['find'],
insert=lambda col, data:
(col, ' // ' + ' // '.join(Cache._uniqueData(list(data), True))),
update=lambda col, data:
(col,
Function.concat(Field(col),
value=' // ' + ' // '.join(
Cache._uniqueData(list(d), True)))),
result=lambda data: data if isinstance(data, list) else list(
filter(None, data.split(' // '))))
}
columns = ['chrom', 'name', 'chromStart', 'chromEnd', 'score', 'strand'
] + cnames
ret, allrest = cache.query(columns, {'name': snps}, dummies)
dbsnp = Genome(db=genome)
dbsnp = getattr(dbsnp, "snp%s" % dbsnpver)
writer = None
if outfile:
head = outopts['head']
headPrefix = outopts['headPrefix']
headDelimit = outopts['headDelimit']
headTransform = outopts['headTransform']
del outopts['head']
del outopts['headPrefix']
del outopts['headDelimit']
del outopts['headTransform']
writer = TsvWriter(outfile, **outopts)
if head:
writer.writeHead(prefix=headPrefix,
delimit=headDelimit,
transform=headTransform)
if writer:
for r in ret.values():
r.CHR = r.chrom
r.START = r.chromStart
r.END = r.chromEnd
r.NAME = r.name
r.SCORE = r.score
r.STRAND = r.strand
writer.write(r)
cached = []
if allrest:
for snp in allrest['name']:
s = dbsnp.filter_by(name=snp).first()
if not s:
if notfound == 'error':
raise RecordNotFound('Record not found: %s' % snp)
elif notfound == 'skip':
continue
else:
stderr.write('Record not found: %s \n' % snp)
continue
cached.append(s)
if writer:
r = TsvRecord()
r.CHR = s.chrom
r.START = s.chromStart
r.END = s.chromEnd
r.NAME = s.name
r.SCORE = s.score
r.STRAND = s.strand
for cname in cnames:
setattr(r, cname, getattr(s, cname))
writer.write(r)
# save cached data
cachedata = {}
for c in cached:
for k in schema.keys():
if not k in cachedata:
cachedata[k] = []
cachedata[k].append(getattr(c, k))
if cachedata:
cache.save(cachedata, dummies)
return {r.name: r for r in ret.values() + cached}
