data_checks
===========

.. py:module:: data_checks

.. autoapi-nested-parse::

   Functions to assure input files for DNAvi are correctly formatted

   Author: Anja Hess

   Date: 2025-JUL-23



Functions
---------

.. autoapisummary::

   data_checks.check_marker_lane
   data_checks.detect_delim
   data_checks.check_name
   data_checks.check_input
   data_checks.check_file
   data_checks.check_ladder
   data_checks.check_meta
   data_checks.check_config
   data_checks.compute_nuc_intervals
   data_checks.check_interval
   data_checks.generate_meta_dict


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

.. py:function:: check_marker_lane(input_nr)

   Quickly check if the number for marker lane is pos
   :param input_nr: int
   :return: int if check passed


.. py:function:: detect_delim(file, num_rows=1)

   Detect delimiter from input table with Sniffer

   :param file: str, path to input file
   :param num_rows: int, number of rows in file
   :return: str, detected delimiter



.. py:function:: check_name(filename)

   Function to generate secure filename from filename

   :param filename: str
   :return: improved file name



.. py:function:: check_input(filename)

   Function to check if the input exists

   :param filename: str

   :return: raise error if file does not exist



.. py:function:: check_file(filename)

   Function to check if file is correctly formatted

   :param filename: str
   :return: raise error if file is incorrectly formatted



.. py:function:: check_ladder(filename)

   Function to check if the ladder is formatted correctly

   :param filename: str
   :return: raise error if file does not have correct format



.. py:function:: check_meta(filename)

   Check if the metadata file is formatted correctly

   :param filename: str, path to metadata file

   :return: raise error if file does not have correct format



.. py:function:: check_config(filename)

   Check if the config file is formatted correctly

   :param filename: str, path to config file

   :return: raise error if file does not have correct format



.. py:function:: compute_nuc_intervals(start, step=200, total_steps=10, prefixes=['Mono', 'Di', 'Tri', 'Tetra', 'Penta', 'Hexa', 'Hepta', 'Octa', 'Nona', 'Deca'])

   Compute interpretable nucleosomaal intervals in format them
   into a common DNAvi nuc dict.

   :param start:
   :param step:
   :param total_steps:
   :param prefixes:
   :return: new nuc_dict (pyhton dictionary)


.. py:function:: check_interval(interval_string, max_val=100000)

   Check if the config file is formatted correctly

   :param filename: str, path to config file

   :return: raise error if file does not have correct format



.. py:function:: generate_meta_dict(meta_path, files=[])

   A function to conveniently parse metadata for multiple files
   when handling multi-file inputs

   :param meta_path: path to metadata file
   :param files: list
   :return: dictionary parsing the new split metadata file for each input file