def generate_hmm_(opts):
fd, tmphmm = mkstemp()
close(fd)
fd, tmpaln = mkstemp()
close(fd)
is_dna = opts.ENCODER == DNAEncoder
try:
with open(opts.REFMSA) as msa_fh:
with open(tmpaln, 'w') as aln_fh:
msa_fmt = seqfile_format(opts.REFMSA)
source = Verifier(SeqIO.parse(msa_fh, msa_fmt), DNAAlphabet)
try:
SeqIO.write((record if is_dna else translate(record)
for record in source), aln_fh, 'stockholm')
except VerifyError:
if is_dna:
raise RuntimeError(
"DNA encoding incompatible with protein reference MSA"
)
source.set_alphabet(AminoAlphabet)
aln_fh.seek(0)
SeqIO.write(source, aln_fh, 'stockholm')
hmmer = HMMER(opts.HMMER_ALIGN_BIN, opts.HMMER_BUILD_BIN)
hmmer.build(tmphmm,
tmpaln,
alphabet=HMMER.DNA if is_dna else HMMER.AMINO)
finally:
if exists(tmpaln):
remove(tmpaln)
return tmphmm
def seqrecords():
is_dna = ARGS.ENCODER == DNAEncoder
seq_fmt = seqfile_format(ARGS.SEQUENCES)
source = Verifier(SeqIO.parse(seq_fh, seq_fmt), DNAAlphabet)
try:
for record in source:
yield record if is_dna else translate(record)
except VerifyError:
if is_dna:
msg = (
"your model specifies a DNA encoding "
"which is incompatible with protein sequences"
)
raise RuntimeError(msg)
source.set_alphabet(AminoAlphabet)
for record in source:
yield record
def seqrecords():
is_dna = ARGS.ENCODER == DNAEncoder
seq_fmt = seqfile_format(ARGS.SEQUENCES)
source = Verifier(SeqIO.parse(seq_fh, seq_fmt), DNAAlphabet)
try:
for record in source:
yield record if is_dna else translate(record)
except VerifyError:
if is_dna:
msg = (
"your model specifies a DNA encoding "
"which is incompatible with protein sequences"
)
raise RuntimeError(msg)
source.set_alphabet(AminoAlphabet)
for record in source:
yield record
def __call__(self, string):
try:
with open(string) as h:
source = Verifier(SeqIO.parse(h, seqfile_format(string)), DNAAlphabet)
try:
seq = next(iter(source))
if not self.is_dna:
seq = translate(seq)
except VerifyError:
if self.is_dna:
raise ArgumentTypeError("DNA encoding incompatible with protein reference")
source.set_alphabet(AminoAlphabet)
seq = next(iter(source))
return seq
except ArgumentTypeError:
raise sys.exc_info()[1]
except:
raise ArgumentTypeError("invalid FASTA file '{0:s}'".format(string))
def __call__(self, string):
try:
with open(string) as h:
source = Verifier(SeqIO.parse(h, seqfile_format(string)),
DNAAlphabet)
try:
seq = next(iter(source))
if not self.is_dna:
seq = translate(seq)
except VerifyError:
if self.is_dna:
raise ArgumentTypeError(
"DNA encoding incompatible with protein reference")
source.set_alphabet(AminoAlphabet)
seq = next(iter(source))
return seq
except ArgumentTypeError:
raise sys.exc_info()[1]
except:
raise ArgumentTypeError(
"invalid FASTA file '{0:s}'".format(string))
def generate_hmm_(opts):
fd, tmphmm = mkstemp(); close(fd)
fd, tmpaln = mkstemp(); close(fd)
is_dna = opts.ENCODER == DNAEncoder
try:
with open(opts.REFMSA) as msa_fh:
with open(tmpaln, 'w') as aln_fh:
msa_fmt = seqfile_format(opts.REFMSA)
source = Verifier(SeqIO.parse(msa_fh, msa_fmt), DNAAlphabet)
try:
SeqIO.write(
(record if is_dna else translate(record) for record in source),
aln_fh,
'stockholm')
except VerifyError:
if is_dna:
raise RuntimeError("DNA encoding incompatible with protein reference MSA")
source.set_alphabet(AminoAlphabet)
aln_fh.seek(0)
SeqIO.write(
source,
aln_fh,
'stockholm')
hmmer = HMMER(opts.HMMER_ALIGN_BIN, opts.HMMER_BUILD_BIN)
hmmer.build(
tmphmm,
tmpaln,
alphabet=HMMER.DNA if is_dna else HMMER.AMINO
)
finally:
if exists(tmpaln):
remove(tmpaln)
return tmphmm
def seqrecords(self, antibodies, clonal=False):
conn = connect(self.__filename)
cur = conn.cursor()
antibodies_ = set(antibodies)
ab_clause = ' or '.join(['ANTIBODY = ?'] * len(antibodies_))
equivalencies = set((next(
cur.execute(
'select distinct ALT_IDS from ANTIBODY where %s' % ab_clause,
tuple(antibodies_)))[0] or '').split(',')) - set([''])
if len(equivalencies):
antibodies_ |= equivalencies
ab_clause = ' or '.join(['ANTIBODY = ?'] * len(antibodies_))
antibodies__ = tuple(sorted(antibodies_))
stmt = dedent('''\
select distinct SG.NO as NO, SG.ID as ID, SG.SEQ as SEQ, SG.SUBTYPE as SUBTYPE, ? as AB, N.VALUE as VALUE from
(select NO, S.ID as ID, SUBTYPE, SEQ from
(select SEQUENCE_NO as NO, SEQUENCE_ID as ID, RAW_SEQ as SEQ from SEQUENCE {0:s} group by ID) as S left join
(select SEQUENCE_ID as ID, SUBTYPE from GENO_REPORT group by ID) as G
on S.ID = G.ID
) as SG join
(select SEQUENCE_ID as ID, ANTIBODY as AB, group_concat(TYPE || ':' || VALUE, ',') as VALUE from NEUT where ({1:s}) group by ID) as N
on SG.ID = N.ID order by SG.ID;
'''.format('where IS_CLONAL = 1' if clonal else '', ab_clause))
params = ('+'.join(antibodies__), ) + antibodies__
cur.execute(stmt, params)
def records():
ids = {}
for row in cur:
nno, sid, seq, subtype, ab, values = row[:6]
values_ = {}
for kv in values.split(','):
k, v = kv.split(':')
try:
v_ = float(v.strip().lstrip('<>'))
except ValueError:
continue
if k not in values_:
values_[k] = []
values_[k].append(v_)
if len(values_) == 0:
warn("skipping sequence '%s', invalid values '%s'" %
(sid, values))
continue
record = SeqRecord(Seq(
OrfList(seq, include_stops=False)[0], DNAAlphabet),
id=sid,
description=json_dumps({
'subtype':
'' if subtype is None else subtype,
'ab':
ab,
'values':
values_
}),
annotations={
'antibody': values_,
'subtype': subtype
})
if sid in ids:
record.id += str(-ids[sid])
ids[sid] += 1
else:
ids[sid] = 1
yield record
source = Verifier(records(), DNAAlphabet)
try:
seqrecords = list(source)
except VerifyError:
source.set_alphabet(AminoAlphabet)
seqrecords = list(source)
conn.close()
return seqrecords, clonal, antibodies__
def seqrecords(self, antibodies, clonal=False):
if clonal:
raise ValueError(
'clonal property is not available with Monogram datasets')
if len(antibodies) > 1:
raise ValueError(
'only one antibody can be interrogated with Monogram datasets')
seqrecords = []
with open(self.__fastafile) as h:
source = Verifier(SeqIO.parse(h, 'fasta'), DNAAlphabet)
try:
seqrecords = list(source)
except VerifyError:
source.set_alphabet(AminoAlphabet)
seqrecords = list(source)
underdash = re_compile(r'[_-](\d+)$')
for r in seqrecords:
r.id = underdash.sub(r'_\1', r.id)
ic50s = dict((r.id, []) for r in seqrecords)
with open(self.__csvfile) as fh:
sample = fh.read(MonogramData.__sample_len)
sniffer = csv_sniffer()
dialect = sniffer.sniff(sample)
if not sniffer.has_header(sample):
raise ValueError(MonogramData.__no_header_msg)
fh.seek(0)
reader = csv_reader(fh, dialect)
columns = None
for i, row in enumerate(reader):
if columns is None:
columns = dict((v.strip(), j) for j, v in enumerate(row))
missing = set(antibodies) - set(columns.keys())
if len(missing):
raise ValueError("antibodies ('%s') not found!" %
"', '".join(missing))
else:
acc = underdash.sub(r'_\1', row[0])
try:
if acc in ic50s:
cln_ic50s = [
float(row[columns[ab]].strip().lstrip('<>'))
for ab in antibodies
if ab in columns and columns[ab] < len(row)
]
ic50s[acc].extend(cln_ic50s)
except:
pass
drop = []
for i, r in enumerate(seqrecords):
if r.id not in ic50s or len(ic50s[r.id]) == 0:
drop.append(i)
warn("skipping sequence '%s', VALUE not found" % r.id)
else:
values = {'IC50': ic50s[r.id]}
r.description = json_dumps({
'ab': antibodies[0],
'values': values
})
r.annotations['antibody'] = values
for i in sorted(drop, reverse=True):
del seqrecords[i]
return seqrecords, clonal, antibodies
def seqrecords(self, antibodies, clonal=False):
conn = connect(self.__filename)
cur = conn.cursor()
antibodies_ = set(antibodies)
ab_clause = ' or '.join(['ANTIBODY = ?'] * len(antibodies_))
equivalencies = set((
next(cur.execute(
'select distinct ALT_IDS from ANTIBODY where %s' % ab_clause,
tuple(antibodies_)
))[0]
or ''
).split(',')) - set([''])
if len(equivalencies):
antibodies_ |= equivalencies
ab_clause = ' or '.join(['ANTIBODY = ?'] * len(antibodies_))
antibodies__ = tuple(sorted(antibodies_))
stmt = dedent('''\
select distinct SG.NO as NO, SG.ID as ID, SG.SEQ as SEQ, SG.SUBTYPE as SUBTYPE, ? as AB, N.VALUE as VALUE from
(select NO, S.ID as ID, SUBTYPE, SEQ from
(select SEQUENCE_NO as NO, SEQUENCE_ID as ID, RAW_SEQ as SEQ from SEQUENCE {0:s} group by ID) as S left join
(select SEQUENCE_ID as ID, SUBTYPE from GENO_REPORT group by ID) as G
on S.ID = G.ID
) as SG join
(select SEQUENCE_ID as ID, ANTIBODY as AB, group_concat(TYPE || ':' || VALUE, ',') as VALUE from NEUT where ({1:s}) group by ID) as N
on SG.ID = N.ID order by SG.ID;
'''.format('where IS_CLONAL = 1' if clonal else '', ab_clause))
params = ('+'.join(antibodies__),) + antibodies__
cur.execute(stmt, params)
def records():
ids = {}
for row in cur:
nno, sid, seq, subtype, ab, values = row[:6]
values_ = {}
for kv in values.split(','):
k, v = kv.split(':')
try:
v_ = float(v.strip().lstrip('<>'))
except ValueError:
continue
if k not in values_:
values_[k] = []
values_[k].append(v_)
if len(values_) == 0:
warn("skipping sequence '%s', invalid values '%s'" % (sid, values))
continue
record = SeqRecord(
Seq(OrfList(seq, include_stops=False)[0], DNAAlphabet),
id=sid,
description=json_dumps({
'subtype': '' if subtype is None else subtype,
'ab': ab,
'values': values_
}),
annotations={'antibody': values_, 'subtype': subtype}
)
if sid in ids:
record.id += str(-ids[sid])
ids[sid] += 1
else:
ids[sid] = 1
yield record
source = Verifier(records(), DNAAlphabet)
try:
seqrecords = list(source)
except VerifyError:
source.set_alphabet(AminoAlphabet)
seqrecords = list(source)
conn.close()
return seqrecords, clonal, antibodies__
def seqrecords(self, antibodies, clonal=False):
if clonal:
raise ValueError('clonal property is not available with Monogram datasets')
if len(antibodies) > 1:
raise ValueError('only one antibody can be interrogated with Monogram datasets')
seqrecords = []
with open(self.__fastafile) as h:
source = Verifier(SeqIO.parse(h, 'fasta'), DNAAlphabet)
try:
seqrecords = list(source)
except VerifyError:
source.set_alphabet(AminoAlphabet)
seqrecords = list(source)
underdash = re_compile(r'[_-](\d+)$')
for r in seqrecords:
r.id = underdash.sub(r'_\1', r.id)
ic50s = dict((r.id, []) for r in seqrecords)
with open(self.__csvfile) as fh:
sample = fh.read(MonogramData.__sample_len)
sniffer = csv_sniffer()
dialect = sniffer.sniff(sample)
if not sniffer.has_header(sample):
raise ValueError(MonogramData.__no_header_msg)
fh.seek(0)
reader = csv_reader(fh, dialect)
columns = None
for i, row in enumerate(reader):
if columns is None:
columns = dict((v.strip(), j) for j, v in enumerate(row))
missing = set(antibodies) - set(columns.keys())
if len(missing):
raise ValueError("antibodies ('%s') not found!" % "', '".join(missing))
else:
acc = underdash.sub(r'_\1', row[0])
try:
if acc in ic50s:
cln_ic50s = [float(row[columns[ab]].strip().lstrip('<>'))
for ab in antibodies
if ab in columns and columns[ab] < len(row)]
ic50s[acc].extend(cln_ic50s)
except:
pass
drop = []
for i, r in enumerate(seqrecords):
if r.id not in ic50s or len(ic50s[r.id]) == 0:
drop.append(i)
warn("skipping sequence '%s', VALUE not found" % r.id)
else:
values = {'IC50': ic50s[r.id]}
r.description = json_dumps({
'ab': antibodies[0],
'values': values
})
r.annotations['antibody'] = values
for i in sorted(drop, reverse=True):
del seqrecords[i]
return seqrecords, clonal, antibodies
