def __init__(self, s=None, ps=None):
if isinstance(s, basestring):
self.sequence = Seq(s)
else:
self.sequence = s
self.prosite = ExPASy.get_prosite_raw(ps)
self.record = Prosite.read(self.prosite)
self.pat = pa.compile(self.record.pattern)
self.regexp = re.compile(pa.prosite_to_re(self.record.pattern))
"{[A-B]}.",
"[{AB}].",
"(A).",
"[A>]-B.",
"A-[<B].",
"A(3,).",
"A(-1).",
#"A(5,2).", # too complicated to check via re
"A(2, 5).",
"A(B,C).",
"A-[<G].",
"[G>]-A.",
"1.",
"[1].",
"[A1B].",
#"[AA].", # too complicated to check via re
"{1}.",
"[<].",
"[>].",
"[A<B].",
"[A>B].",
)
for pat in bad_patterns:
print pat, "-",
try:
Pattern.compile(pat)
except TypeError:
print "correctly failed"
else:
print "INCORRECTLY PASSED"
"{[A-B]}.",
"[{AB}].",
"(A).",
"[A>]-B.",
"A-[<B].",
"A(3,).",
"A(-1).",
#"A(5,2).", # too complicated to check via re
"A(2, 5).",
"A(B,C).",
"A-[<G].",
"[G>]-A.",
"1.",
"[1].",
"[A1B].",
#"[AA].", # too complicated to check via re
"{1}.",
"[<].",
"[>].",
"[A<B].",
"[A>B].",
)
for pat in bad_patterns:
print pat, "-",
try:
Pattern.compile(pat)
except TypeError:
print "correctly failed"
else:
print "INCORRECTLY PASSED"