validate

Command validate checks gff consistency and performs statistics.

usage

$ ingenannot -v 2 validate genes.gff -s -g genome.fasta

positional arguments:

Gff_genes

Gene Annotation file in GFF/GTF file format

optional arguments:

-h, –help	show this help message and exit
-s, –statistics	Statistics of annotations
-g GENOME, –genome GENOME	Genome in Fasta file, more statistics metrics if provided
-a, –addseqs	Export file in GFF3 with ##sequence-region pragma
–fixframe	fix error in CDS frame and log warning
–gaeval	Perform required control and transform to run with gaeval
-o OUTPUT, –output OUTPUT	Output Annotation file in GFF file format

inputs

Gff_genes in GFF/GTF format. Common errors in annotation files are missing Parent or missing ID on some features.

outputs

The first goal of validate is to ensure the structure of your gff/gtf file with required info/tags. If you specify the -s option you get statitistics on your annotations and more with -g.

## Statistics ##
nb_genes;12635
average_gene_length;1443.0950534230312
median_gene_length;1158
min_gene_length;143
max_gene_length;29360
nb_transcripts;12635
average_transcripts_per_gene;1.0
average_transcript_length;1443.0950534230312
median_transcript_length;1158
min_transcript_length;143
max_transcript_length;29360
nb_exons;35603
average_exons_per_transcript;2.8178076770874556
average_exon_length;445.75858775945846
median_exon_length;214
min_exon_length;3
max_exon_length;20704
nb_transcript_mono_exon;3094
nb_introns;22968
average_introns_per_transcript;1.8178076770874554
average_intron_length;102.88936781609195
median_intron_length;63
min_intron_length;40
max_intron_length;5775
nb_CDS;12635
nb_complete_CDS;12635
nb_partial_CDS;0
average_CDS_length;1256.0417095370003
median_CDS_length;999
min_CDS_length;102
max_CDS_length;29232
nb_transcripts_with_utr;1
average_five_prime_utr_length;90.0
median_five_prime_utr_length;90
min_five_prime_utr_length;90
max_five_prime_utr_length;90
average_three_prime_utr_length;164.0
median_three_prime_utr_length;164
min_three_prime_utr_length;164
max_three_prime_utr_length;164
################