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())
