Fetch genomic context from a GenBank file

What it does

This script reads a GenBank file and, given a label, it will try to find a matching qualifier. If found, it will extract it, plus some extra bps upstream/downstream (default: 20 kbps)

Notes

• The label must be complete (no fuzzy search)
• The script only looks at CDS features
• Qualifiers where the label will be searched for: gene, protein_id, proteinId, locus_tag and name
• If the extension falls in the middle of a CDS feature, it will be stretched as far as needed to completely include the CDS
• The extracted locus is reverse-complemented if the targeted feature is in the reverse strand
• Output is also a GenBank file
• For even more control at each side, use the --downstream and --upstream paramteres

Usage:

usage: fetch_context_gbk.py [-h] -i INPUT -l LABEL [-e EXTRA] [-u UPSTREAM] [-d DOWNSTREAM] [-o OUTPUTFOLDER]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        GenBank file
  -l LABEL, --label LABEL
                        Target label (gene_id, locus_tag, etc.)
  -e EXTRA, --extra EXTRA
                        Number of bps at either side of the target gene/protein/locus_tag to extract. Default=20000
  -u UPSTREAM, --upstream UPSTREAM
                        Override extension upstream of target with desired bps
  -d DOWNSTREAM, --downstream DOWNSTREAM
                        Override extension downstream of target by desired bps
  -o OUTPUTFOLDER, --outputfolder OUTPUTFOLDER
                        Where to put retrieved files. Default=output

Requirements

• Python 3
• biopython