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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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DRAM.py merge_annotations error, not recognizing argument #231

Closed STraving closed 1 year ago

STraving commented 1 year ago

Hi DRAM team.

Thanks for a great tool! I'm analyzing viral sequences from metagenomic samples and processing them using DRAMv. I ran DRAM.py distill on each separate sample. I then became aware of the merge_annotations function but it throws me an error, maybe I misunderstand what the function really is for and using it wrong? My folder structure is: /xx/xx/DRAM_test/sample1/sample1_annotations.tsv /xx/xx/DRAM_test/sample2/sample2_annotations.tsv

my command and the output:

DRAM.py merge_annotations -i /work/work/sachia_56data/DRAM_test/* -o /work/work/sachia_56data/DRAM_combined/
usage: DRAM.py [-h]
               {annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations}
               ...
DRAM.py: error: unrecognized arguments: /work/work/sachia_56data/DRAM_test/Site_9_1-3

bottom line, is there a way a to somehow merge all my annotations before I distill them - or merge the distilled output in an easy way? If not that's also okay, I'll make it work :)

Thanks again for a great tool!

Cheers, Sachia

rmFlynn commented 1 year ago

Can you try DRAM.py "merge_annotations -i /work/work/sachia_56data/DRAM_test/*" -o /work/work/sachia_56data/DRAM_combined/?

rmFlynn commented 1 year ago

The wild card needs to have quotes to pass a string, sometimes, otherwise bash will pass its interpretation of the wild card.

STraving commented 1 year ago

Hi Rory, Thank you! The following worked: DRAM.py merge_annotations -i "/work/work/sachia_56data/DRAM_test/*" -o /work/work/sachia_56data/DRAM_combined1/

Thank you so much for solving this. Have a nice Friday and weekend!

Cheers, Sachia