def testIsValid(self):
# Valid
self.assertTrue(FastqIO.isValid(self.tmp_seq))
self.assertTrue(FastqIO.isValid(self.tmp_seq_gz))
# Valid long file
content = "@seq1\nATGC\n+\n####\n@seq2\nATGC\n+\n####\n@seq3\nATGC\n+\n####\n@seq4\nATGC\n+\n####\n@seq5\nATGC\n+\n####\n@seq6\nATGC\n+\n####\n@seq7\nATGC\n+\n####\n@seq8\nATGC\n+\n####\n@seq9\nATGC\n+\n####\n@seq10\nATGC\n+\n####\n@seq11\nATGC\n+\n####\n"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastqIO.isValid(self.tmp_out))
# Valid empty file
content = ""
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastqIO.isValid(self.tmp_out))
# Valid empty sequence
content = "@seq1\n\n+\n\n"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastqIO.isValid(self.tmp_out))
# Invalid file (fasta)
content = ">seq1\nATGC\n>seq2\nATGC"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(not FastqIO.isValid(self.tmp_out))
# Invalid file (not a sequence)
content = "@seq1\nAT1GC2\n+\n######"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(not FastqIO.isValid(self.tmp_out))
def testWrite(self):
with FastqIO(self.tmp_out, "w") as FH_out:
for curr_rec in self.expected_rec:
FH_out.write(curr_rec)
self.assertTrue(FastqIO.isValid(self.tmp_out))
self.assertTrue(filecmp.cmp(self.tmp_out, self.tmp_seq))