The mitoz tools gbfiletool command

A tool to deal with Genbank records, to cut out some regions from the GenBank file, to get complement and reverse the GenBank file, to re-order the beginning gene of a circular mitogenome, and to output specific GenBank record.

$ mitoz-tools gbfiletool -h
usage: mitoz-tools gbfiletool [-h] {cut,comrev,sort,select} ...

A tool to deal with genbank records: cut, comrev, sort and select

Version
    0.0.1

Author
    mengguanliang@genomics.cn, BGI.

Please cite:
Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu,
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation
and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkz173

positional arguments:
  {cut,comrev,sort,select}
    cut                 cutting sequences (5' and/or 3' end).
    comrev              get complement reverse of genbank records
    sort                sort the gene orders (input should all be circular records!!!)
    select              output specific genbank records

optional arguments:
  -h, --help            show this help message and exit

sort

This assumes your mitogenome is circular.

$ mitoz-tools gbfiletool sort -h
usage: mitoz-tools gbfiletool sort [-h] -i <STR> -o <STR> -g <STR>

optional arguments:
  -h, --help  show this help message and exit
  -g <STR>    the first gene in output

input/output arguments:
  -i <STR>    genbank input file
  -o <STR>    genbank out file