antismash_scripts

How to run

Gather assemblies in fasta_folder
run prokka on all isolates using:
. activate env_prokka
python3 /srv/data/tools/git.repositories/antismash_scripts/batch_prokka.py [fasta_folder] [prokka_output_folder]
wait for prokka to finish on all isolates, then run antismash on all isolates:
conda deactivate
. activate env_antismash
python3 /srv/data/tools/git.repositories/antismash_scripts/batch_antismash_prokkaout.py [prokka_output_folder] [antismash_output_folder]
rename bigscape output gbk files:
python3 /srv/data/tools/git.repositories/antismash_scripts/copy_antismash_output.py [antismash_output_folder] [bigscape_input_folder]
run BiG-SCAPE
python3 /srv/data/tools/git.repositories/BiG-SCAPE/bigscape.py -i [bigscape_input_folder] -o [bigscape_output_folder]

Name		Name	Last commit message	Last commit date
Latest commit History 38 Commits
refseq_bigscape		refseq_bigscape
.DS_Store		.DS_Store
._antismash_summary.R		._antismash_summary.R
._copy_antismash_output.py		._copy_antismash_output.py
._summarize_GCF_presence_absence.py		._summarize_GCF_presence_absence.py
README.md		README.md
antismash_summary.R		antismash_summary.R
batch_antismash.py		batch_antismash.py
batch_antismash_prokkaout.py		batch_antismash_prokkaout.py
batch_prokka.py		batch_prokka.py
copy_antismash_output.py		copy_antismash_output.py
copy_random_files.py		copy_random_files.py
gather_gbf_from_prokka.py		gather_gbf_from_prokka.py
gather_gff_from_prokka.py		gather_gff_from_prokka.py
summarize_GCF_presence_absence.py		summarize_GCF_presence_absence.py