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Package Bio :: Package Prosite :: Module Pattern :: Class PrositeMatch |
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Method Summary | |
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__init__(self,
prosite,
seq,
match)
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__getitem__(self,
i)
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__getslice__(self,
i,
j)
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__len__(self)
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__repr__(self)
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__str__(self)
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end(self,
g)
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group(self,
*groups)
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groups(self,
default)
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returns the specific Prosite pattern used to find this sequence | |
return a list of numbers mapping to items of the original pattern | |
span(self,
g)
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start(self,
g)
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Method Details |
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mapped_pattern(self)returns the specific Prosite pattern used to find this sequence>>> p = Prosite.compile("[AP](2,3)-D.") >>> m = p.search(Seq.Seq("PAD")) >>> mapping = m.mapping() >>> mapped = m.mapped_pattern() >>> print str(m[1]), str(p[mapping[1]]), str(mapped[1]) P [AP](2,3) [AP] >>> print str(mapped) [AP]-[AP]-D. >>>Note that the original term includes the count, while the mapped pattern does the expansion. |
mapping(self)return a list of numbers mapping to items of the original pattern For example, if the Prosite pattern is "[AP](2)-D." matched against "PAD", then the mapping is [1, 1, 2], meaning the first character of the match ("P") is from the first Prosite group ("[AP]"), as is the second letter ("A"). The 3rd letter ("D") is mapped to group 2 of the pattern. |
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