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from Bio.Prosite import Pattern
from Bio import Seq
unchanged_patterns = (
("A.", ("A", "BA"), ("B", "BBP", "")),
("x.", ("A", "BA", "B"), ("",)),
("{A}.", ("B", "BBP"), ("A", "AAA", "")),
("[AB].", ("AB", "PA", "PPAB", "PPABP", "B"), ("C", "CCCCCCFDS")),
("{AB}.", ("C", "CDFDC"), ("", "A", "B", "BA", "BAB")),
("A-B.", ("AB", "AACAB", "ABAAA"), ("BA", "PPDAAPB", "A", "B")),
("A-x.", ("AB", "AACAB", "ABAAA"), ("BA", "A", "B")),
("[AB]-[BC].", ("AB", "AC", "BB", "BC"), ("BA", "CA", "A", "C", "PPQ")),
("[AB]-[BC]-[CD].", ("ABC", "QACD", "QBBCQ"), ("ABA", "A", "DCB")),
("[AB]-[BC]-[CDEFGHIKLMN].", ("ABC", "ACN"), ("AB", "PERPPWPTW")),
("{AB}-[BC]-[CD].", ("CCC", "CCD", "QCCCP"), ("ABC",)),
("[AB]-{BC}-[CD].", ("AAD", "APD", "QBACP"), ("ABC", "PAAEQ")),
("[AB]-[BC]-{CD}.", ("ABA", "ABP", "QBBAP"), ("ABC", "PAAE")),
("{AB}-[BC]-{CD}.", ("CCB", "PBP"), ("ABA", "PACR")),
("A-B-C-D.", ("QABCDQ",), ("ABCP",)),
("<A.", ("ABC", "A"), ("PAB", "BAAAAAA")),
("<{A}.", ("PAB", "BAAAAAA"), ("ABC", "A")),
("<[AB].", ("A", "B", "AP", "BBQ"), ("QBB", "PA")),
("<{AB}.", ("QBB", "PA"), ("A", "B", "AP", "BBQ")),
("<A-B.", ("AB", "ABB"), ("BAB", "PABQ")),
("<[AB]-[BC].", ("AB", "AC", "BB", "BC"), ("PAB", "QBB", "PPPPPQABBCAC")),
("<[AB]-[BC]-[CD].", ("ABC", "ACC"), ("CCD", "Q", "QPPAABC")),
("<[AB]-[BC]-[CDEFGHIKLMN].", ("ABC", "BBN"), ("QABC", "PBBN", "PPQ")),
("<{AB}-[BC]-[CD].", ("CCC", "QBDQ"), ("ABD", "PDD")),
("<[AB]-{BC}-[CD].", ("AEC", "APD"), ("CDD", "AEE", "ACC", "QAEC")),
("<[AB]-[BC]-{CD}.", ("ABB",), ("ABC", "QABB")),
("<{AB}-[BC]-{CD}.", ("CBB",), ("ABA", "QCDB")),
("A>.", ("A", "BA", "AA", "QQQA"), ("AB", "AAAAB")),
("{A}>.", ("B", "AB", "AAAQ"), ("A", "BA", "QQQQQQA")),
("[AB]>.", ("A", "B", "AB", "QQA"), ("Q", "AQ", "BQ", "ABQ")),
("{AB}>.", ("Q", "AQ", "BQ", "ABQ"), ("A", "B", "AB", "QQA")),
("A-B>.", ("AB", "QAB"), ("ABA", "ABQ", "BA")),
("[AB]-[BC]>.", ("AB", "AC", "BB", "BC"), ("ABQ", "ACQ", "Q", "QQQ")),
("[AB]-[BC]-[CD]>.", ("ABC", "BBD", "QABC"), ("ABCQ", "BBDQ", "QQQ")),
("[AB]-[BC]-[CDEFGHIKLMN]>.", ("ABN", "QQABN"), ("ABB", "BBB", "ACCD")),
("{AB}-[BC]-[CD]>.", ("CCC", "CCD"), ("CCDQ", "Q")),
("[AB]-{BC}-[CD]>.", ("AAC", "QBQD"), ("AACQ", "Q")),
("[AB]-[BC]-{CD}>.", ("ABB", "QABE"), ("ACBQ", "QABEQ", "P")),
("{AB}-[BC]-{CD}>.", ("CCA", "AAACCA"), ("CCAC", "AAACCAD")),
("<A>.", ("A",), ("B", "AA", "BAB", "BA", "AB")),
("<{A}>.", ("B", "C"), ("A", "BC", "BC", "AA")),
("<[AB]>.", ("A", "B"), ("C", "AB", "BA", "AA", "BB", "Q")),
("<{AB}>.", ("C", "Q"), ("A", "B", "AB", "AC", "BA")),
("<A-B>.", ("AB", ), ("AAB", "ABB", "Q", "QABQ")),
("<[AB]-[BC]>.", ("AB", "BB", "BC", "AC"), ("PAB", "ABQ", "QABQ")),
("<[AB]-[BC]-[CD]>.", ("ABC", "BBD"), ("QABC", "ABCQ", "QABCQ", "QQ")),
("<[AB]-[BC]-[CDEFGHIKLMN]>.", ("ABC", "ACI", "BCN"), ("QABC", "ABCQ",
"QACI", "ACIQ", "QACIQ", "Q", "QQQ")),
("<{AB}-[BC]-[CD]>.", ("CCC", "CBC", "QCD"), ("CCCC", "QCDC", "QCDQ")),
("<[AB]-{BC}-[CD]>.", ("AAD", "AQC"), ("QAAD", "AADQ", "QAAD", "QQQ")),
("<[AB]-[BC]-{CD}>.", ("ABB", "BBB"), ("QABB", "BABQ")),
("<{AB}-[BC]-{CD}>.", ("CCA", "FCF"), ("QQQQ", "QCCAQ", "Q")),
("A-[BC>].", ("AB", "AC", "A"), ("AQ", "Q")),
("<A-[BC>].", ("AB", "AC", "A"), ("AA", "AQ", "Q")),
("A-[BC>]>.", ("AB", "AC", "A"), ("ABQ",)),
("[<AB]-C.", ("C", "AC", "BC", "ABC"), ("QCC", "AB")),
("[<AB]-[CD>].", ("", "QA", "AB", "QADQ", "QAB", "ADQ", "QQB", "QQBDQ",
"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)
mapped_pattern = m.mapped_pattern()
offset = m.start()
for i in range(len(mapped_pattern)):
mpi = mapped_pattern[i]
#print "***", str(x[offset+i]), str(mpi)
if mpi.ignore:
assert x[offset+i] not in mpi.letters, repr(mpi.letters)
else:
if mpi.letters != "x":
assert x[offset+i] in mpi.letters, repr(mpi.letters)
for x in bad_list:
if p.search(Seq.Seq(x)) is not None:
print "\t", "should be bad group re, but succeeded:", repr(x)
bad_patterns = (
"A",
"A<",
">A",
"A<.",
">A.",
"[AB]<.",
">[AB].",
"AB.",
"A-B<.",
"A(B).",
"A.B",
"A.B.",
"A-B",
"[A-B]",
"{[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"
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