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))
