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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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cazy annotation format for version 1.4.6 #338

Closed Ales-ibt closed 6 months ago

Ales-ibt commented 6 months ago

Hello there!

Thank you for developing DRAm, it is a great tool and I've enjoyed playing around with its functionalities, in particular, with DRAM distil. I managed to generate nice visuals using my own functional annotation with dram version 1.3. But now that I upgraded the container to v1.4.6 I just cannot figure out how do the cazy annotation should be formatted in the annotations.tsv file. Looking at the code, I think now it requires cazy_best_hit (and maybe in a separate column cazy_ids?). The description of the columns for annotation.tsv in the wiki is not detailed enough.

I have tried different combinations but I just cannot manage to get the plot with cazy annotations. The rest of the annotations are displayed correctly.

Could you guys please provide an example of the annotation.tsv output for version 1.4.6 so I can mimic the format? That would save me the effort to download and format all the databases to generate an example.

Thanks in advance!

Ales-ibt commented 6 months ago

I managed to generate an example. This is the header of the annotations.tsv for v1.4.6 in case someone else finds it useful:

fasta scaffold gene_position start_position end_position strandedness rank ko_id kegg_hit peptidase_id peptidase_family peptidase_hit peptidase_RBH peptidase_identity peptidase_bitScore peptidase_eVal pfam_hits cazy_ids cazy_hits cazy_subfam_ec cazy_best_hit heme_regulatory_motif_count