deepbiop.fq
===========

.. py:module:: deepbiop.fq


Classes
-------

.. autoapisummary::

   deepbiop.fq.EncoderOption
   deepbiop.fq.FastqDataset
   deepbiop.fq.FastqIterator
   deepbiop.fq.FastqRecord
   deepbiop.fq.ParquetEncoder
   deepbiop.fq.Predict
   deepbiop.fq.RecordData


Functions
---------

.. autoapisummary::

   deepbiop.fq.convert_multiple_fqs_to_one_fq
   deepbiop.fq.encode_fq_path_to_parquet
   deepbiop.fq.encode_fq_path_to_parquet_chunk
   deepbiop.fq.encode_fq_paths_to_parquet
   deepbiop.fq.encode_qual
   deepbiop.fq.fastq_to_fasta
   deepbiop.fq.get_label_region
   deepbiop.fq.load_predicts_from_batch_pt
   deepbiop.fq.load_predicts_from_batch_pts
   deepbiop.fq.select_record_from_fq
   deepbiop.fq.select_record_from_fq_by_random
   deepbiop.fq.test_predicts
   deepbiop.fq.write_fq
   deepbiop.fq.write_fq_parallel


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

.. py:class:: EncoderOption

   .. py:property:: qual_offset
      :type: int



   .. py:property:: bases
      :type: list[int]



   .. py:property:: threads
      :type: int



.. py:class:: FastqDataset

   .. py:method:: __len__()


   .. py:method:: __getitem__(idx)


   .. py:method:: __iter__()


   .. py:method:: from_file(file_path, chunk_size)
      :staticmethod:



   .. py:method:: get_stats()


   .. py:method:: get_records(start, end)


   .. py:method:: get_records_indexed(start, end)


   .. py:method:: get_records_sequential(start, end)


.. py:class:: FastqIterator

   .. py:method:: __iter__()


   .. py:method:: __next__()


.. py:class:: FastqRecord

   .. py:property:: header
      :type: str



   .. py:property:: sequence
      :type: str



   .. py:property:: quality
      :type: str



   .. py:method:: __repr__()


.. py:class:: ParquetEncoder

.. py:class:: Predict

   A struct to store the prediction result.


   .. py:property:: prediction
      :type: list[int]



   .. py:property:: seq
      :type: str



   .. py:property:: id
      :type: str



   .. py:property:: is_truncated
      :type: bool



   .. py:property:: qual
      :type: str | None



   .. py:method:: __repr__()


   .. py:method:: prediction_region()

      Get the prediction region.



   .. py:method:: smooth_prediction(window_size)

      Get the smooth prediction region.



   .. py:method:: smooth_label(window_size)

      Get the smooth label.



   .. py:method:: smooth_and_select_intervals(smooth_window_size, min_interval_size, append_interval_number)

      Smooth and select intervals.



   .. py:method:: seq_len()

      Get the sequence length.



   .. py:method:: qual_array()

      Get the quality score array.



   .. py:method:: show_info(smooth_interval, text_width = None)

      Show the information of the prediction.



   .. py:method:: __getstate__()


   .. py:method:: __setstate__(state)


.. py:class:: RecordData

   .. py:property:: id
      :type: str



   .. py:property:: seq
      :type: str



   .. py:property:: qual
      :type: str



.. py:function:: convert_multiple_fqs_to_one_fq(paths, result_path, parallel)

.. py:function:: encode_fq_path_to_parquet(fq_path, bases, qual_offset, result_path = None)

.. py:function:: encode_fq_path_to_parquet_chunk(fq_path, chunk_size, parallel, bases, qual_offset)

.. py:function:: encode_fq_paths_to_parquet(fq_path, bases, qual_offset)

.. py:function:: encode_qual(qual, qual_offset)

   Convert ASCII quality to Phred score for Phred+33 encoding.


.. py:function:: fastq_to_fasta(fastq_path, fasta_path)

.. py:function:: get_label_region(labels)

.. py:function:: load_predicts_from_batch_pt(pt_path, ignore_label, id_table)

.. py:function:: load_predicts_from_batch_pts(pt_path, ignore_label, id_table, max_predicts = None)

.. py:function:: select_record_from_fq(selected_reads, fq, output)

.. py:function:: select_record_from_fq_by_random(fq, number, output)

.. py:function:: test_predicts(predicts)

.. py:function:: write_fq(records_data, file_path = None)

.. py:function:: write_fq_parallel(records_data, file_path, threads)