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())