tfclass_predict.sequence_processor
==================================

.. py:module:: tfclass_predict.sequence_processor


Classes
-------

.. autoapisummary::

   tfclass_predict.sequence_processor.SequenceProcessor


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

.. py:class:: SequenceProcessor(tokenizer, genome)

   Class for processing sequences.


   .. py:attribute:: tokenizer


   .. py:attribute:: genome


   .. py:method:: extract_fasta_sequences(chromosome, start_str, end_str, desired_length=150)

      Extracts a genomic sequence of a specified length from the provided chromosome coordinates.
      Standardizes chromosome names and adjusts coordinates to ensure the sequence meets the desired length.

      :param chromosome: Chromosome coordinates in hg38.
      :param start_str: Start of the sequence in bp.
      :param end_str: End of the sequence in bp.
      :param desired_length: Length of the sequence in bp.
      :return: A genomic sequence of the specified length.



   .. py:method:: sequence_to_kmers(sequence, k=6)

      Splits a string into defined kmers.
      :param sequence: String to split.
      :param k: kmer size.
      :return: List of kmers.



   .. py:method:: kmers_to_tokens(kmers, max_length=15)

      Converts kmers into tokens using DNABERT.
      :param kmers: List of kmers.
      :param max_length: Max length of tokens.
      :return: List of tokens.