rename
Command rename renames gene names.
usage
$ ingenannot -v 2 rename genes.gff G_{geneidx:05}0 --locus_tag --mapping
positional arguments:
Gff_genes |
Gene Annotation file in GFF/GTF file format |
pattern |
Pattern to use for renaming gene, {ref}=sequence, {geneidx}=gene index whole genome, {geneidxref}= gene index on the sequence |
optional arguments:
-h, –help |
show this help message and exit |
–mapping |
Export mapping file to keep track of changes |
–locus_tag |
Add gene Id as Locus_tag for ENA submission |
–name |
Replace the tag Name in Gene and mRNA feature with new ID |
–tr_ranking_ID |
In cases of multi-mRNA, try to keep the order based on name ex T001.1 then T001.2 when renaming |
inputs
Gff_genes in GFF/GTF format. Patterns and expected results for 2 genes on 2 different chromosomes (chr1, chr2):
pattern |
result |
|---|---|
G_{geneidx} |
G_1 / G_2 |
G_{geneidx:05} |
G_00001 / G_00002 |
G_{geneidx:05}0 |
G_000010 / G_000020 |
{ref}_G_{geneidx:05}0 |
chr1_G_000010 / chr_2G_000020 |
G_{ref}_{geneidxref:05}0 |
G_chr1_000010 / G_chr2_000010 |
outputs
Renamed Gff file and gene / transcript mapping file if –mapping option.