https://github.com/gamcil/genome2json

Parse GenBank/GFF3 to JSON
https://github.com/gamcil/genome2json

Last synced: about 1 year ago
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Parse GenBank/GFF3 to JSON

• Host: GitHub
• URL: https://github.com/gamcil/genome2json
• Owner: gamcil
• License: mit
• Created: 2020-01-28T11:00:14.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2020-10-30T05:12:52.000Z (over 5 years ago)
• Last Synced: 2025-04-16T01:00:07.451Z (about 1 year ago)
• Language: Python
• Size: 73.2 KB
• Stars: 3
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# genome2json

Parse genomes in GenBank/GFF3 format to JSON

Implemented in pure Python using builtin libraries.

```

$ g2j -h

usage: Genome2JSON [-h] (-gbk GENBANK | -gff GENERAL) [-fa FASTA] -o OUTPUT

                   [--json_indent JSON_INDENT] [--grouped]

Parse genomes in GenBank/GFF3 format, and convert to JSON

optional arguments:

  -h, --help            show this help message and exit

  -gbk GENBANK, --genbank GENBANK

                        GenBank file

  -gff GENERAL, --general GENERAL

                        GFF3 file

  -fa FASTA, --fasta FASTA

                        FASTA file, required when parsing GFF

  -o OUTPUT, --output OUTPUT

                        Save JSON to file

  --json_indent JSON_INDENT

                        Number of spaces to indent in JSON

  --grouped             Group overlapping sequence features

Cameron Gilchrist 2020

```