The arguments used in the `/main/src/disease_analysis.py` file
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This file contains details about the Disease Analysis arguments.
The default arguments for this script are as follows:
cmd = ' '.join(['python3', 'disease_analysis.py',
'--context-name', '"{}"'.format(context_name),
'--config-file', '"{}"'.format(disease_config_file),
'--data-source', '"{}"'.format(data_source),
'--taxon-id', '"{}"'.format(taxon_id)])
!{cmd}
| Argument | Required? | Default Value | Description |
|---|---|---|---|
--config-file |
Yes | None |
The path to the configuration file specified under/main/data/config_sheets/disease/diease_data_inputs_<tissue_name> |
--context-name |
Yes | None |
The type of context being used (i.e., naiveB, smB, etc.) |
--data-source |
Yes | None |
Source of data being used, either rnaseq or microarray |
--taxon-id |
No | 9096 |
BioDbNet taxon ID number, also accepts ‘human’, or ‘mouse’ |