python/convert_dates_to_days/README.md

In msk-access/access_data_analysis: ACCESS data analysis

Convert Dates to Days

Tool to do the following operations:

• Reads meta data file, and based on the timepoint information given, convert them to days for a samples belonging to a given patient_id
• Supports following date formats:
• MM/DD/YY
• M/D/YY
• MM/D/YY
• M/DD/YY
• MM/DD/YYYY
• YYYY/MM/DD

Requirements

• pandas
• typing
• arrow

Example command

python convert_dates_to_days.py -i ./example_input.txt -t2 "SCREEN"

Usage

> python convert_dates_to_days.py --help
Usage: convert_dates_to_days.py [OPTIONS]

  Tool to do the following operations: A. Reads meta data file, and based on
  the timepoint information given convert them to days for a samples
  belonging to a given patient_id B. Supports following date formats:
  'MM/DD/YY','M/D/YY','MM/D/YY','M/DD/YY','MM/DD/YYYY','YYYY/MM/DD'

  Requirement: pandas; typer; arrow

Options:
  -i, --input FILE        Input file with the information to convert dates to
                          days  [required]

  -t1, --timepoint1 TEXT  Column name which has timpoint information to use
                          the baseline date, first preference  [default: C1D1]

  -t2, --timepoint2 TEXT  Column name which has timpoint information to use
                          the baseline date, second preference  [default: ]

  -o, --output TEXT       Name of the output file  [default: output.txt]
  --install-completion    Install completion for the current shell.
  --show-completion       Show completion for the current shell, to copy it or
                          customize the installation.

  --help                  Show this message and exit.

msk-access/access_data_analysis documentation built on Nov. 13, 2023, 12:43 p.m.