Input arguments

The SOPRANO pipeline can be run from the command line with soprano-run. Arguments can be passed explicitly via their flag-to-value definitions, or within an argument definition file.

Argument definitions

Required arguments

These arguments have short (-s) or long (--long) argument flags.

-n | --name

The name of the SOPRANO pipeline run.

-o | --output

The path to the output file directory (i.e. the cache) for the SOPRANO pipeline run.

-i | --input

The path to the input VEP annotated file that defines mutations.

-b | --bed_file

The path to the bed file containing protein coordinates named by their transcript ID (e.g. ENSTXXXXXX 123 135)

Optional arguments

These arguments have short (-s) or long (--long) argument flags.

-m | --random_regions

The path to the bed file that defines regions for randomization. Defaults to None, implying arbitrary randomization.

-x | --seed

The seed value to be used in randomization process. If defined, users should be able to reproduce their results when randomization is applied. This value should be an integer greater than zero. Defaults to "-1", implying no seed value chosen.

-s | --species

The Latin species name associated with genome reference. The default value is for homo_sapiens.

-a | --assembly

The name of the Ensembl reference genome assembly. The default value is for GRCh38 (Homo Sapiens).

-r | --release

The Ensembl release number of the genome reference file. The default value is 110.

-t | --transcript

Path to transcript lengths.

-p | --protein_transcript

Path to protein transcript lengths.

-f | --fasta

Path to ensembl transcript IDs (fasta file).

Optional switches

These switches are activated by passing the long (--long) flag to the command line with no subsequent argument. They alter the runtime behaviour of SOPRANO.

--use_random

Run SOPRANO with randomization. Note that if random_regions are passed, to the CLI, this overrides the selection to use_random to True.

--use_ssb192

Run SOPRANO using SSB192 substitutions, otherwise defaults SSB7.

--keep_drivers

Run SOPRANO with driver genes included. Otherwise, data/aux_soprano/genes2exclude.txt are excluded.