deepbiop.core
=============

.. py:module:: deepbiop.core


Functions
---------

.. autoapisummary::

   deepbiop.core.generate_kmers
   deepbiop.core.generate_kmers_table
   deepbiop.core.kmers_to_seq
   deepbiop.core.normalize_seq
   deepbiop.core.reverse_complement
   deepbiop.core.seq_to_kmers


Module Contents
---------------

.. py:function:: generate_kmers(base, k)

   Generate all possible k-mers from a set of base characters.

   This function takes a string of base characters and a k-mer length,
   and generates all possible k-mer combinations of that length.

   # Arguments

   * `base` - A string containing the base characters to use (e.g. "ATCG")
   * `k` - The length of k-mers to generate

   # Returns

   A vector containing all possible k-mer combinations as strings


.. py:function:: generate_kmers_table(base, k)

   Generate a lookup table mapping k-mers to unique IDs.

   This function takes a string of base characters and a k-mer length,
   and generates a HashMap mapping each possible k-mer to a unique integer ID.

   # Arguments

   * `base` - A string containing the base characters to use (e.g. "ATCG")
   * `k` - The length of k-mers to generate

   # Returns

   A HashMap mapping k-mer byte sequences to integer IDs


.. py:function:: kmers_to_seq(kmers)

   Convert k-mers back into a DNA sequence.

   This function takes a vector of k-mers and reconstructs the original DNA sequence.
   The k-mers are assumed to be in order and overlapping.

   # Arguments

   * `kmers` - A vector of k-mers as `String`s

   # Returns

   The reconstructed DNA sequence as a `String`, wrapped in a `Result`


.. py:function:: normalize_seq(seq, iupac)

   Normalize a DNA sequence by converting any non-standard nucleotides to standard ones.

   This function takes a DNA sequence as a `String` and a boolean flag `iupac` indicating whether to normalize using IUPAC ambiguity codes.
   It returns a normalized DNA sequence as a `String`.

   # Arguments

   * `seq` - A DNA sequence as a `String`.
   * `iupac` - A boolean flag indicating whether to normalize using IUPAC ambiguity codes.

   # Returns

   A normalized DNA sequence as a `String`.


.. py:function:: reverse_complement(seq)

   Generate the reverse complement of a DNA sequence.

   This function takes a DNA sequence as a `String` and returns its reverse complement.
   The reverse complement is generated by reversing the sequence and replacing each nucleotide
   with its complement (A<->T, C<->G).

   # Arguments

   * `seq` - A DNA sequence as a `String`

   # Returns

   The reverse complement sequence as a `String`

   # Example

   ```
   use deepbiop_core::seq::reverse_complement;

   let seq = String::from("ATCG");
   let rev_comp = reverse_complement(seq);
   assert_eq!(rev_comp, "CGAT");
   ```


.. py:function:: seq_to_kmers(seq, k, overlap)

   Convert a DNA sequence into k-mers.

   This function takes a DNA sequence and splits it into k-mers of specified length.
   The sequence is first normalized to handle non-standard nucleotides.

   # Arguments

   * `seq` - A DNA sequence as a `String`
   * `k` - The length of each k-mer
   * `overlap` - Whether to generate overlapping k-mers

   # Returns

   A vector of k-mers as `String`s