splitgbk

This is a super simple script that performs only one task:

• Given a genbank file with multiple sequences, it splits it into multiple files, each one with one sequence and its related annotation features.

CLI help message

A very simple script to split multisequence genbank files into separate files
Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
License: Public Domain

usage:
    falmeida-py splitgbk
    falmeida-py splitgbk [ -h|--help ]
    falmeida-py splitgbk [ --gbk <file> ] [ --outdir <outdir> ]

options:
    -h --help                               Show this screen.
    -g --gbk=<file>                         Input genbank file to split into multiple individual files.
    -o --outdir=<outdir>                    Directory (must already exist) in which to write the splitted files [Default: ./].
falmeida-py: a package to the simple distribution of my custom scripts.

Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
License: Public Domain

usage:
    falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
    falmeida-py <command> [ -h|--help ] [ <args>... ]

options:
    -h --help                  Show this screen
    -v --version               Show version information
    --license                  Show LEGAL LICENSE information

commands:
    tsv2markdown               Command for rapid convertion of tsv or csv to markdown tables.
    splitgbk                   Command to split multisequence genbank files into individual files.
    align2subsetgbk            Command to subset genbank files based on alignments to a FASTA file.
    gbk2fasta                  Command to convert genbank files to fasta files.
    blasts                     Command to execute automatized blast commands.
    replace_fasta_seq          Command to replace strings in a FASTA using defitinitions from a BED file
    mpgap2csv                  Command to summarize main mpgap multiqc assembly statistics into a CSV file
    bacannot2json              Command to summarize main bacannot annotation results into JSON file

Use: `falmeida-py <commmand> -h` to get more help and see examples.

Usage

The usage is super simple:

falmeida-py tsv2markdown --gbk multi_contig.gbk --outdir single_contig_gbks

Note

The directory must already exist.