GEO datasets

Publically available datasets with the sample information provided in .soft and .miniml file formats. This script is currently being created specific to one such dataset - Mammals Methylation Consortium

soft_2_csv

Parses the .soft file into a csv sample_sheet containing information about each entry. Also stores that information as a list of dictionaries

load_soft

Includes functions .soft file into a list of lines and creates a .pkl file to reload lines if needed.

read_series_data

Extremely specific for this particular dataset. In the function parse_txt_file add line numbers to get more columns.

usage: read_series_data.py [-h] [-x] [-c] input_file

script to extract required information from the sample_matrix file
positional arguments:
  input_file  Path to the input file
options:
  -h, --help  show this help message and exit
  -x, --xlsx  creates excel file
  -c, --csv   creates csv file```