[−][src]Struct pattern_partition_prediction::PaPaPredIndel
Implementations
impl PaPaPredIndel
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pub fn new<P: AsRef<Path>>(
path: P,
min_kmer_size: Option<usize>
) -> Result<Self, Error>
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path: P,
min_kmer_size: Option<usize>
) -> Result<Self, Error>
Create a PaPaPredIndel instance.
Note that this class treats insertions and deletions the same, hence "indel". But it distinguishes between outframe (=frameshift) and inframe (non-frameshift) mutations.
The input file must consist of 3 space-separated columns:
- The pattern in UIPAC notation.
- The probability for a frameshift indel
- The probability for a non-frameshift indel
You provide the path
to the sequence-context point mutation probabilities file.
If you want to ensure that the patters have a minimum size, you can provide a value for
min_kmer_size
which will pad all patterns with Ns at the end. The minimum kmer size has
to be an even number because the insertion or deletion should happen right in the middle
of the sequence
pub fn rates(&self, seq: &str) -> Result<IndelTransitionProbabilities, Error>
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Query the mutation rates for a sequence context
The indel is assumed to happen inbetween the two middle nuleotides
pub fn kmer_size(&self) -> usize
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pub fn radius(&self) -> usize
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Auto Trait Implementations
impl RefUnwindSafe for PaPaPredIndel
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impl Send for PaPaPredIndel
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impl Sync for PaPaPredIndel
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impl Unpin for PaPaPredIndel
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impl UnwindSafe for PaPaPredIndel
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Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized,
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T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized,
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T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
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T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T
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impl<T> From<T> for T
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impl<T, U> Into<U> for T where
U: From<T>,
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U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>,
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U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>
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impl<T, U> TryInto<U> for T where
U: TryFrom<T>,
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U: TryFrom<T>,