class SeqLoader(MultiprocessingBase, FilenameParser):
fasta_re = re.compile(r'.*\.f(asta|as|a|aa|fn|rn|na)$')
schemas = {
'fasta': fasta_re,
'gb': re.compile(r'.*\.gb(ff|k)$'),
'embl': re.compile(r'.*\.embl$'),
}
def __init__(self, abort_event):
super(SeqLoader, self).__init__(abort_event)
dna_letters = set(ambiguous_dna_letters.upper())
rna_letters = set(ambiguous_rna_letters.upper())
protein_letters = set(extended_protein_letters.upper())
@classmethod
def guess_alphabet(cls, seq):
letters = set(seq[:10].upper()) # use just first 10 letters
nletters = len(letters)
if len(letters.intersection(cls.dna_letters)) == nletters:
return generic_dna
if len(letters.intersection(cls.protein_letters)) == nletters:
return generic_protein
return generic_alphabet
@classmethod
def correct_alphabet(cls, seq):
cls._set_alphabet(seq, cls.guess_alphabet(seq))
return seq
@classmethod
def _set_alphabet(cls, rec, abc):
rec.seq.alphabet = abc
return rec
@classmethod
def load_file(cls, filename, schema=None, guess_alphabet=False):
if not os.path.isfile(filename):
print 'No such file: %s' % filename
return None
if not schema: schema = cls.guess_schema(filename)
try:
if guess_alphabet:
recs = list(
cls.correct_alphabet(rec)
for rec in SeqIO.parse(filename, schema))
else:
recs = list(SeqIO.parse(filename, schema))
return recs
except Exception, e:
print 'Unable to parse %s as %s\n%s' % (filename, schema, str(e))
return None
def test_fastq_dna(self):
"""Read and write back simple example with ambiguous DNA"""
#First in upper case...
data = "@%s\n%s\n+\n%s\n" \
% ("id descr goes here",
ambiguous_dna_letters.upper(),
"".join(chr(33+q) for q in range(len(ambiguous_dna_letters))))
handle = StringIO()
self.assertEqual(1, SeqIO.write(SeqIO.parse(StringIO(data), "fastq"), handle, "fastq"))
self.assertEqual(data, handle.getvalue())
#Now in lower case...
data = "@%s\n%s\n+\n%s\n" \
% ("id descr goes here",
ambiguous_dna_letters.lower(),
"".join(chr(33+q) for q in range(len(ambiguous_dna_letters))))
handle = StringIO()
self.assertEqual(1, SeqIO.write(SeqIO.parse(StringIO(data), "fastq"), handle, "fastq"))
self.assertEqual(data, handle.getvalue())
def test_fastq_dna(self):
"""Read and write back simple example with ambiguous DNA"""
#First in upper case...
data = "@%s\n%s\n+\n%s\n" \
% ("id descr goes here",
ambiguous_dna_letters.upper(),
"".join(chr(33+q) for q in range(len(ambiguous_dna_letters))))
handle = StringIO("")
self.assertEqual(1, SeqIO.write(SeqIO.parse(StringIO(data), "fastq"), handle, "fastq"))
self.assertEqual(data, handle.getvalue())
#Now in lower case...
data = "@%s\n%s\n+\n%s\n" \
% ("id descr goes here",
ambiguous_dna_letters.lower(),
"".join(chr(33+q) for q in range(len(ambiguous_dna_letters))))
handle = StringIO("")
self.assertEqual(1, SeqIO.write(SeqIO.parse(StringIO(data), "fastq"), handle, "fastq"))
self.assertEqual(data, handle.getvalue())
