Extract Ti/Ri plasmid and genes

Extract Ti/Ri oncogenic plasmid based on BEAV output

What is does

• Look for all known Ti/Ri genes in the GenBank file generated by BEAV
• Extract individual Ti/Ri genes and save them in .ffa & .faa format
• Summarize known Ti/Ri genes predicted by BEAV in .gff3 format
• Extract the whole oncogenic plasmid(s) in a seperate GenBank file

Usage

python3 extract_ti.py [-h] --input INPUT --contiglist CONTIGLIST

Alternatively, you can submit an SGE job using the wrapper provided in the SGE_wrapper/run_extract_ti.sh directory. Use the following command:

./run_extract_ti.sh path/to/BEAV/output/dir

Arguments

• --input: A GenBank file generated by BEAV
• --contiglist: *.oncogenic_plasmid_final.out.contiglist file that contains all predicted contigs to be oncogenes

Output

• Ti genes extracted and written in: *.ti_genes.ffn/fna files
• Ti gene extraction summary written in: *.ti_genes.gff3
• Ti plasmid extracted and saved in: *.ti_plasmid.gbk

To do

• Update bash wrapper script.
• Set up dedicated output directory.