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object --+ | FormattedSeq
FormattedSeq(seq, [linear=True])-> new FormattedSeq. Translate a Bio.Seq into a formatted sequence to be used with Restriction. Roughly: remove anything which is not IUPAC alphabet and then add a space in front of the sequence to get a biological index instead of a python index (i.e. index of the first base is 1 not 0). Retains information about the shape of the molecule linear (default) or circular. Restriction sites are search over the edges of circular sequence.
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circularise FS |
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linearise FS |
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new linear FS instance |
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new circular FS instance |
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bool |
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list |
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Inherited from |
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Inherited from |
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FormattedSeq(seq, [linear=True])-> new FormattedSeq. seq is either a Bio.Seq, Bio.MutableSeq or a FormattedSeq. if seq is a FormattedSeq, linear will have no effect on the shape of the sequence.
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repr(x)
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return a list of pattern into the sequence. the list is made of tuple (location, pattern.group). the latter is used with non palindromic sites. pattern is the regular expression pattern corresponding to the enzyme restriction site. size is the size of the restriction enzyme recognition-site size.
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