def antibodies(self):
antibodies = []
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)
# grab everything after the accession column in the header row
for row in reader:
antibodies.extend(r.strip() for r in row[1:])
break
return antibodies
def antibodies(self):
antibodies = []
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)
# grab everything after the accession column in the header row
for row in reader:
antibodies.extend(r.strip() for r in row[1:])
break
return 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+)$')
for r in seqrecords:
r.id = underdash.sub(r'_\1', r.id)
ic50s = dict((r.id, []) for r in seqrecords)
with open(self.__csvfile) as fh:
sample = fh.read(MonogramData.__sample_len)
sniffer = csv_sniffer()
dialect = sniffer.sniff(sample)
if not sniffer.has_header(sample):
raise ValueError(MonogramData.__no_header_msg)
fh.seek(0)
reader = csv_reader(fh, dialect)
columns = None
for i, row in enumerate(reader):
if columns is None:
columns = dict((v.strip(), j) for j, v in enumerate(row))
missing = set(antibodies) - set(columns.keys())
if len(missing):
raise ValueError("antibodies ('%s') not found!" %
"', '".join(missing))
else:
acc = underdash.sub(r'_\1', row[0])
try:
if acc in ic50s:
cln_ic50s = [
float(row[columns[ab]].strip().lstrip('<>'))
for ab in antibodies
if ab in columns and columns[ab] < len(row)
]
ic50s[acc].extend(cln_ic50s)
except:
pass
drop = []
for i, r in enumerate(seqrecords):
if r.id not in ic50s or len(ic50s[r.id]) == 0:
drop.append(i)
warn("skipping sequence '%s', VALUE not found" % r.id)
else:
values = {'IC50': ic50s[r.id]}
r.description = json_dumps({
'ab': antibodies[0],
'values': values
})
r.annotations['antibody'] = values
for i in sorted(drop, reverse=True):
del seqrecords[i]
return seqrecords, clonal, antibodies
def seqrecords(self, antibodies, clonal=False):
if clonal:
raise ValueError('clonal property is not available with Monogram datasets')
if len(antibodies) > 1:
raise ValueError('only one antibody can be interrogated with Monogram datasets')
seqrecords = []
with open(self.__fastafile) as h:
source = Verifier(SeqIO.parse(h, 'fasta'), DNAAlphabet)
try:
seqrecords = list(source)
except VerifyError:
source.set_alphabet(AminoAlphabet)
seqrecords = list(source)
underdash = re_compile(r'[_-](\d+)$')
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