filter

ìngenannot filter filters genes based on annotations in gff (TE, …).

usage

$ ingenannot -v 2 filter genes.gff TE.gff genes.noTE.gff -f match -r 0.2

positional arguments:

Gff_genes

Gene Annotation file in GFF/GTF file format

Gff_TEs

Annotation file in GFF/GTF file format

Output

Output Annotation file in GFF file format

optional arguments:

-h, –help

show this help message and exit

-s SIZE, –size SIZE

Minimum required size of feature for filtering, default=300bp

-f FEATURE, –feature FEATURE

Feature type expected for filtering, default=match_part

–bed

Bed file expected instead of GFF/GTF file

-r FRACTION, –fraction FRACTION

Minimum fraction of CDS overlapped for filtering, default=0.1 (10 percent)

inputs

Gff_genes in GFF/GTF format. GFF_TEs or bed file, with features to take into account to filter the gene file

outputs

Filtered gff file, with only gene structures with gene, mRNA, exon and CDS features. UTRs are removed.