... | ... | @@ -41,12 +41,16 @@ create_update_kegg_ko | Create or update all KEGG KO from KEGG API. |
|
|
|
|
|
###### EggNOG
|
|
|
|
|
|
* create_update_eggnog
|
|
|
* create_eggnog_functional_cat
|
|
|
Script | description
|
|
|
------ | -----------
|
|
|
create_update_eggnog | Create or update all EggNOG entries from annotations.tsv file
|
|
|
create_eggnog_functional_cat | Create or update all EggNOG functional categories from COG_functional_categories.txt file.
|
|
|
|
|
|
###### Taxonomy
|
|
|
|
|
|
* build_hierarchy
|
|
|
Script | description
|
|
|
------ | -----------
|
|
|
build_hierarchy | Build hierarchy for taxonomy entries.
|
|
|
|
|
|
##### Import genes
|
|
|
|
... | ... | @@ -54,17 +58,23 @@ create_update_kegg_ko | Create or update all KEGG KO from KEGG API. |
|
|
|
|
|
###### IGC
|
|
|
|
|
|
* import_igc_annotation
|
|
|
* import_igc_sequences
|
|
|
Script | description
|
|
|
------ | -----------
|
|
|
import_igc_annotation | Create or update IGC genes from IGC annotations file
|
|
|
import_igc_sequences | Add IGC gene sequences to corresponding genes
|
|
|
|
|
|
###### Virgo
|
|
|
|
|
|
* import_virgo_eggnog
|
|
|
* import_virgo_genes
|
|
|
* import_virgo_kegg
|
|
|
* import_virgo_sequences
|
|
|
* import_virgo_taxonomy
|
|
|
Script | description
|
|
|
------ | -----------
|
|
|
import_virgo_genes | Create or update all Virgo genes (name and length from `0.geneLength.txt` file)
|
|
|
import_virgo_eggnog | Create or update all EggNOG annotation for Virgo genes (from `3.eggnog.NOG.txt` file)
|
|
|
import_virgo_kegg | Create or update all KEGG annotation for Virgo genes (from `8.A.kegg.ortholog.txt` file)
|
|
|
import_virgo_sequences | Create or update all Virgo gene equences (from `NT.fasta` file)
|
|
|
import_virgo_taxonomy | Create or update all Taxonomy annotations for Virgo genes (from `1.taxon.tbl.txt` file)
|
|
|
|
|
|
#### Pre computed metrics
|
|
|
|
|
|
* compute_stats |
|
|
Script | description
|
|
|
------ | -----------
|
|
|
compute_stats | Compute gene catalog statistics |