data_checks
Functions to assure input files for DNAvi are correctly formatted
Author: Anja Hess
Date: 2025-JUL-23
Functions
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Quickly check if the number for marker lane is pos |
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Detect delimiter from input table with Sniffer |
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Function to generate secure filename from filename |
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Function to check if the input exists |
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Function to check if file is correctly formatted |
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Function to check if the ladder is formatted correctly |
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Check if the metadata file is formatted correctly |
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Check if the config file is formatted correctly |
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Compute interpretable nucleosomaal intervals in format them |
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Check if the config file is formatted correctly |
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A function to conveniently parse metadata for multiple files |
Module Contents
- data_checks.check_marker_lane(input_nr)
Quickly check if the number for marker lane is pos :param input_nr: int :return: int if check passed
- data_checks.detect_delim(file, num_rows=1)
Detect delimiter from input table with Sniffer
- Parameters:
file – str, path to input file
num_rows – int, number of rows in file
- Returns:
str, detected delimiter
- data_checks.check_name(filename)
Function to generate secure filename from filename
- Parameters:
filename – str
- Returns:
improved file name
- data_checks.check_input(filename)
Function to check if the input exists
- Parameters:
filename – str
- Returns:
raise error if file does not exist
- data_checks.check_file(filename)
Function to check if file is correctly formatted
- Parameters:
filename – str
- Returns:
raise error if file is incorrectly formatted
- data_checks.check_ladder(filename)
Function to check if the ladder is formatted correctly
- Parameters:
filename – str
- Returns:
raise error if file does not have correct format
- data_checks.check_meta(filename)
Check if the metadata file is formatted correctly
- Parameters:
filename – str, path to metadata file
- Returns:
raise error if file does not have correct format
- data_checks.check_config(filename)
Check if the config file is formatted correctly
- Parameters:
filename – str, path to config file
- Returns:
raise error if file does not have correct format
- data_checks.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.
- Parameters:
start
step
total_steps
prefixes
- Returns:
new nuc_dict (pyhton dictionary)
- data_checks.check_interval(interval_string, max_val=100000)
Check if the config file is formatted correctly
- Parameters:
filename – str, path to config file
- Returns:
raise error if file does not have correct format
- data_checks.generate_meta_dict(meta_path, files=[])
A function to conveniently parse metadata for multiple files when handling multi-file inputs
- Parameters:
meta_path – path to metadata file
files – list
- Returns:
dictionary parsing the new split metadata file for each input file