bananabenana

#!/usr/bin/env python
# Slices/subsections genbank files by either gene names or base pair range. This handles multi-genbank files which have multiple contigs

# Usage:
#   slice_multi_genbank.py -i infile.gbk -g gene1:gene2 -o gene_sliced_output.gbk # This will extract the region between two genes including these genes
#   slice_multi_genbank.py -i infile.gbk -g gene1:gene2 -n 2 -o gene_sliced_output.gbk # This will extract 2 genes up- and down-stream of your specified two genes
#   slice_multi_genbank.py -i infile.gbk -g gene1: -o gene_extract_output.gbk # This will extract a single gene
#   slice_multi_genbank.py -i infile.gbk -g gene1: -n 3 -o gene_extract_output.gbk # This will extract a single gene and 3 genes up- and down-stream of the gene
#   slice_multi_genbank.py -i infile.gbk -r start:end:contig -o range_sliced_output.gbk # This will slice via base pair range and locus/contig. This is required to handle multi-genbank files