Add locus tags to the GenBank or EMBL files

One of the main reasons to create this script is to supplement files annotated with RASTtk pipeline from the PATRIC web service with locus tags as they are absent from the standard output.

The locus tags are required for EMBL annotated assembly submisson and for work of some packages.

Requirements

The only requirement is BioPython.

Input

The script accepts files in GenBank and EMBL formats. Details are in the "The DDBJ/ENA/GenBank Feature Table Definition" document.

Output

Output is the same GenBank or EMBL file with added /locus_tag fields to the feature keys that require locus tags. Feature keys that require locus tags are specified according to the "The DDBJ/ENA/GenBank Feature Table Definition", 7.2 Appendix II: Feature keys reference.

The locus tag is formed by prefix and number with fixed number of positions. For numbers that has less positions than specified in --len_num argument leading zeroes will be added.

For example with --prefix BA --len_num 4 the locus tags will be: BA_0001, BA_0002, ..., BA_0748, ..., BA_3984.

Usage

usage: add_lt.py [-h] [-f FILE] [-n IN_TYPE] [-u OUT_TYPE] [-o OUT] [-p PREFIX] [-l LEN_NUM]

Adds locus_tag field to the GBK or EMBL files.

optional arguments:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  Path to the input file.
  -n IN_TYPE, --in_type IN_TYPE
                        Input file type. Values: "gb" (Default) or "embl".
  -u OUT_TYPE, --out_type OUT_TYPE
                        Input file type. Values: "gb" (Default) or "embl".
  -o OUT, --out OUT     Path to the output file.
  -p PREFIX, --prefix PREFIX
                        Locus_tag prefix.
  -l LEN_NUM, --len_num LEN_NUM
                        Length of the numeric part of the locus tag. Default: 5

Example:

python3 add_lt.py -f Input.gbk --in_type gb --out_type gb -o Output.gbk -p BACT -l 5 

The locus tags would be: BACT_00001 BACT_00002 BACT_00003 ...