def testIsValid(self):
# Valid
self.assertTrue(FastaIO.isValid(self.tmp_mono_line))
self.assertTrue(FastaIO.isValid(self.tmp_multi_line))
self.assertTrue(FastaIO.isValid(self.tmp_multi_line_gz))
# Valid long file
content = ">seq1\nATGC\n>seq2\nATGC\n>seq3\nATGC\n>seq4\nATGC\n>seq5\nATGC\n>seq6\nATGC\n>seq7\nATGC\n>seq8\nATGC\n>seq9\nATGC\n>seq10\nATGC\n>seq11\nATGC\n>seq12\nATGC"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastaIO.isValid(self.tmp_out))
# Valid empty file
content = ""
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastaIO.isValid(self.tmp_out))
# Valid empty sequence
content = ">seq1\n"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastaIO.isValid(self.tmp_out))
# Invalid file (two headers)
content = ">seq1\nATGC\n>seq2\n>seq3\nATGC"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(not FastaIO.isValid(self.tmp_out))
# Invalid file (no header at the first line)
content = "seq1\nATGC\n>seq2\nATGC"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(not FastaIO.isValid(self.tmp_out))
# Invalid file (fastq)
content = "@seq1\nATGC\n+\n####"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(not FastaIO.isValid(self.tmp_out))
def testWrite(self):
with FastaIO(self.tmp_out, "w") as FH_out:
for curr_rec in self.expected_rec:
FH_out.write(curr_rec)
self.assertTrue(FastaIO.isValid(self.tmp_out))
self.assertTrue(filecmp.cmp(self.tmp_out, self.tmp_mono_line))