gff toolbox overview

About

This command uses BCBio package to get the gist of an input GFF file.

Help message

# Trigger help
gff-toolbox overview -h

# Help
gff-toolbox:

            Overview

This command uses BCBio library to let you get the gist of your GFF file

usage:
    gff-toolbox overview [ -h|--help ] [ --input <gff> ]

options:
    -h, --help                                               Show this screen
    -i, --input=<gff>                                        Input GFF file. GFF file must not contain sequences with it. [Default: stdin]

example:

    ## Getting the overview of a generic GFF file

$ gff-toolbox overview -i Athaliana_ref.gff.gz

$ gff-toolbox overview -i Kp_ref.gff

Execution

# Example
gff-toolbox overview -i Kp_ref.gff

# Output
Input: Kp_ref.gff gff file.

Overview:

{
    'gff_id': {
        ('NC_016838.1', ): 290,
        ('NC_016839.1', ): 305,
        ('NC_016840.1', ): 9,
        ('NC_016841.1', ): 3,
        ('NC_016845.1', ): 10982,
        ('NC_016846.1', ): 321,
        ('NC_016847.1', ): 11,
    },
    'gff_source': {('RefSeq', ): 11921},
    'gff_source_type': {
        ('RefSeq', 'CDS'): 5779,
        ('RefSeq', 'exon'): 88,
        ('RefSeq', 'gene'): 5867,
        ('RefSeq', 'rRNA'): 25,
        ('RefSeq', 'region'): 7,
        ('RefSeq', 'sequence_feature'): 92,
        ('RefSeq', 'tRNA'): 62,
        ('RefSeq', 'tmRNA'): 1,
    },
    'gff_type': {
        ('CDS', ): 5779,
        ('exon', ): 88,
        ('gene', ): 5867,
        ('rRNA', ): 25,
        ('region', ): 7,
        ('sequence_feature', ): 92,
        ('tRNA', ): 62,
        ('tmRNA', ): 1,
    },
}