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Imported modules
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from NeedlemanWunsch import nw
from chimera.Sequence import Sequence
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Functions
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constrainedMatch
dragMatch
gappedMatch
makeForcedMatch
nwAssoc
oldTryAssoc
tryAssoc
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constrainedMatch
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constrainedMatch (
aseq,
mseq,
segments,
maxErrors,
)
all the segments should fit in aseq
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Exceptions
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AssertionError, "Internal match problem: segments (%d) != offsets (%d)" %(len( segments ), len( offsets ) )
ValueError, "bad assoc"
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dragMatch
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dragMatch (
aseq,
gappedMseq,
maxErrors,
)
mseq longer than aseq
can still be gaps in mseq
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gappedMatch
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gappedMatch (
aseq,
mseq,
segments,
gaps,
estLen,
maxErrors,
)
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makeForcedMatch
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makeForcedMatch (
side,
aseq,
mseq,
aseqStart,
aseqLength,
mseqStart,
mseqLength,
)
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nwAssoc
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nwAssoc ( alignSeq, molSeq )
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oldTryAssoc
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oldTryAssoc (
alignSeq,
molSeq,
gappedMseq,
maxErrors=6,
)
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tryAssoc
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tryAssoc (
alignSeq,
mseq,
segments,
gaps,
estLen,
maxErrors=6,
)
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Classes
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Matchup | When done, self.best will either be None or a 3-tuple.
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