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))
"C", "B", "CQ"), ("Q", "QQ", "QAQ", "QC", "AQ", "QCQ")),
("[<ABC>].", ("", "A", "AQ", "QA", "QAQ"), ()),
# Some ranges
("A(3).", ("AAA", "AAAB", "AAAAA", "BAAA"), ("AA", "AABA", "BBB", "")),
("x(3).", ("AAA", "BBB", "ABC"), ("AA", "B", "")),
("A(3)-B(3).", ("AAABBB", "BBBAAABBB"), ("ABABABAB", "AABBB")),
("A(2,3)-B(1,3).", ("AABB", "AAB", "AABBB", "AAAB"), ("ABBB", "QQQQQ")),
("A-x(1,5)-B.", ("ABB", "ABBBBBB", "ACCCCCB", "ACB"), ("ACCCCCCB", "AB")),
("[AB](3,4).", ("AAA", "AAAA", "ABAB", "BABA", "BBAB"), ("ABC", "CBA",
"QQQQ")),
("{AB}(3,5)-A(2).", ("CCCAA", "QCQAQCQAAQ"), ("ABAAA", )),
)
for pattern, good_list, bad_list in unchanged_patterns:
p = Pattern.Prosite(pattern=pattern)
print "Patterns:", repr(pattern), repr(p.re.pattern), \
repr(p.grouped_re.pattern)
assert p.tostring() == pattern, (p.tostring(), pattern)
for x in good_list:
if p.re.search(x) is None:
print "\t", "should be good re, but failed:", repr(x)
for x in bad_list:
if p.re.search(x) is not None:
print "\t", "should be bad re, but succeeded:", repr(x)
for x in good_list:
m = p.search(Seq.Seq(x))
if m is None:
print "\t", "should be good group re, but failed:", repr(x)
else:
#print "x=", repr(x)
"{[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"
