json2gff - Convert JSON to GFF

Overview

New in version 0.2.6.

This script converts annotations in JSON format that were created using MGKit back into GFF annotations.

mongodb command

Annotations converted into MongoDB records with get-gff-info mongodb can be converted back into a GFF file using this command. It can be useful to get a GFF file as output from a query to a MongoDB instance on the command line.

For example:

mongoexport -d db -c test | json2gff mongodb

will convert all the annotations in the database db, collection test to the standard out.

Options

Convert JSON to GFF

usage: json2gff [-h] [-v | --quiet] [--cite] [--manual] [--version]
                {mongodb,json} ...

Named Arguments

-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit

Sub-commands:

mongodb

Convert annotations from a MongoDB instance to GFF

json2gff mongodb [-h] [-v | --quiet] [--cite] [--manual] [--version]
                 [input_file] [output_file]

Positional Arguments

input_file	Input file, defaults to stdin Default: -
output_file	Output file, defaults to stdout Default: <open file ‘<stdout>’, mode ‘w’ at 0x7fa31cd94150>

Named Arguments

-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit

json

Convert annotations from JSON lines to GFF

json2gff json [-h] [-v | --quiet] [--cite] [--manual] [--version]
              [input_file] [output_file]

Positional Arguments

input_file	Input file, defaults to stdin Default: -
output_file	Output file, defaults to stdout Default: <open file ‘<stdout>’, mode ‘w’ at 0x7fa31cd94150>

Named Arguments

-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit