diff --git a/src/nplinker/genomics/bigscape/runbigscape.py b/src/nplinker/genomics/bigscape/runbigscape.py index b685cddf..50f9b0eb 100644 --- a/src/nplinker/genomics/bigscape/runbigscape.py +++ b/src/nplinker/genomics/bigscape/runbigscape.py @@ -28,6 +28,7 @@ def run_bigscape( The directory can contain subdirectories, in which case BiG-SCAPE will search recursively for GBK files. E.g.: + ``` example_folder ├── organism_1 │  ├── organism_1.region001.gbk @@ -38,6 +39,7 @@ def run_bigscape( ├── organism_2 │  ├── ... └── ... + ``` By default, only GBK Files with "cluster" or "region" in the filename are accepted. GBK Files with "final" in the filename are excluded. @@ -56,6 +58,10 @@ def run_bigscape( FileNotFoundError: If the antismash_path does not exist or if the BiG-SCAPE python script could not be found. RuntimeError: If BiG-SCAPE fails to run. + Examples: + >>> from nplinker.genomics.bigscape import run_bigscape + >>> run_bigscape(antismash_path="./antismash", output_path="./output", + ... extra_params="--help", version=1) """ # switch to correct version of BiG-SCAPE if version == 1: