Struct pattern_partition_prediction::PaPaPredIndel

pub struct PaPaPredIndel { /* fields omitted */ }

Implementations

impl PaPaPredIndel

pub fn new<P: AsRef<Path>>(
    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:

1. The pattern in UIPAC notation.
2. The probability for a frameshift indel
3. 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>

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

pub fn radius(&self) -> usize