usage: python -m tcr_pmhc_interface_analysis.apps.sample_ots
[-h] [--sample-size SAMPLE_SIZE] [--num NUM] [--seed SEED]
[--redundant] [--columns COLUMNS [COLUMNS ...]] --output OUTPUT
[--log-level {debug,info,warning,error}]
path
Sample OTS sequences and select columns.
positional arguments:
path path to OTS files
options:
-h, --help show this help message and exit
--sample-size SAMPLE_SIZE
size of samples (Default: 1000)
--num NUM, -n NUM number of samples to take (Default: 1)
--seed SEED Seed for sampling (Default: None)
--redundant do not remove redundant TCRs based on input columns
--columns COLUMNS [COLUMNS ...]
relevant columns to include (Default: cdr1_aa_alpha,
cdr2_aa_alpha, cdr3_aa_alpha, cdr1_aa_beta,
cdr2_aa_beta, cdr3_aa_beta, v_call_alpha, v_call_beta,
j_call_alpha, j_call_beta)
--output OUTPUT, -o OUTPUT
path to output csv
Logging:
Options for logging
--log-level {debug,info,warning,error}
Level to log messages at (Default: 'warning')