slice_multi_gbk

Slices/subsections genbank files by either gene names, locus tags or base pair range. This handles multi-genbank files which have multiple contigs. Outputs sub-setted genbank files as well as multifasta CDS and amino acid files.

Requirements

• biopython >1.84

Installation

Easiest to create a mamba/conda environment

mamba create -y -n slice_gbk_env
mamba install -y -n slice_gbk_env conda-forge::biopython=1.84

Test script

mamba activate slice_gbk_env
python slice_multi_gbk.py -h

Quick start

# Extract the region between two genes including these genes
python slice_multi_gbk.py -i infile.gbk -g gene1:gene2 -o gene_sliced_output # using gene names
python slice_multi_gbk.py -i infile.gbk -g gene1:gene2 -o gene_sliced_output -p # using gene names, also outputting multifasta protein and CDS files with sliced genbank
python slice_multi_gbk.py -i infile.gbk -lt locus_tag1:locus_tag2 -o locus_tag_sliced_output # using locus tags

# Extract 2 genes up- and down-stream of your specified two genes
python slice_multi_gbk.py -i infile.gbk -g gene1:gene2 -n 2 -o gene_sliced_output # using gene names
python slice_multi_gbk.py -i infile.gbk -lt locus_tag1:locus_tag2 -n 2 -o locus_tag_sliced_output # using locus tags

# Extract a single gene
python slice_multi_gbk.py -i infile.gbk -g gene1: -o gene_extract_output # using gene names
python slice_multi_gbk.py -i infile.gbk -lt locus_tag1: -o locus_tag_sliced_output # using locus tags

# Use a wildcard to extract gene/s
python slice_multi_gbk.py -i infile.gbk -g gene*: -o wildcard_gene_extract_output # using gene names
python slice_multi_gbk.py -i infile.gbk -lt locus_tag*: -o wildcard_gene_extract_output # using locus tags

# Extract a single gene and 3 genes up- and down-stream of the gene
python slice_multi_gbk.py -i infile.gbk -g gene1: -n 3 -o gene_extract_output # using gene names
python slice_multi_gbk.py -i infile.gbk -lt locus_tag: -n 3 -o gene_extract_output # using locus tags

# Extract a base pair range from contig. Contig name required to handle multi-genbank files
python slice_multi_gbk.py -i infile.gbk -r start:end:contig -o range_sliced_output

Usage and options

Command	Decsription	Example
-i/--infile	Input genbank file. Required
-g/--genes	The one/two gene names to slice between (inclusive). Handles wildcards (*).	Single gene: -g hemF:. Between two genes: -g hemF:maeB
-lt/--locus_tags	One/two locus tags of gene to slice between (inclusive). Handles wildcards (*)	Single gene: -lt DKHHJM_01915:. Between two genes: -lt DKHHJM_01915:DKHHJM_01920
-n/--num_genes	Number of genes to slice before and after the selected genes. Will take maximum number of genes up/downstream if at end of a contig. Used with -g or -lt. Default=0	Two genes up and downstream: -n 2
-r/--range	Two base pair coordinates (range) to slice between. Contig name or locus must be provided. Used instead of -g or -lt. Optional	Slicing contig_1 between bp 612899-630276: -r 612899:630276:contig_1
-o/--outfile	Output directory and filename prefix. Required	Name output E_coli: -o E_coli
-p/--protein	Produce multifasta files for nucleotide (CDS) and amino acid sequences contained within sliced genbanks. Optional	Get multifasta: -p
-c/--case_insensitive	Turn OFF case sensitivity for gene and locus tag matching. Optional	Turn off case sensitivity: -c
-v/--version	Get version of script. Run alone	Get version: -v

Authors

• Ben Vezina
  • Scholar: https://scholar.google.com/citations?user=Rf9oh94AAAAJ&hl=en&oi=ao
  • ORCID: https://orcid.org/0000-0003-4224-2537
• Abhinaba Ray
• Adapted from https://gist.github.com/jrjhealey/2df3c65c7a70cbca4862e94620e4d7b2