Correct syntax for the program "DRAM.py merge_annotations"

[psampara]

Hello, I am trying to run "DRAM.py merge_annotations" program on individually annotated bins, but the program is unable to recognize the contents of the directories. Could you help me understand the correct syntax to run the "merge_annotations" program on previously annotated individual bins?

I have my annotations in the directory "/08_dram/annotations" and each subdirectory in this folder is an individually annotated bin. An example path of the annotations for a bin in the parent directory is: "08_dram/annotations/annotation_bin.500"

I tried "merge" annotations in different ways -

1. DRAM.py merge_annotations -i /08_dram/annotations/* -o /08_dram/merge_anno This code resulted in the following error:

usage: DRAM.py [-h] {annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations} ... DRAM.py: error: unrecognized arguments: annotations/annotation_bin.123/ annotations/annotation_bin.125/ ... and so on listing all directories in the "/08_dram/annotations" directory.

2. I also tried to run without the wildcard "*" in the above code as such: DRAM.py merge_annotations -i /08_dram/annotations/ -o /08_dram/merge_anno But it resulted in the following error:

2023-08-03 10:45:44,074 - The log file is created at merge_anno/annotate.log 2023-08-03 10:45:44,075 - Skipping the fallowing directory because no 'annotations.tsv' file was found: /scratch/st-ziels-1/psampara/pao_sip/08_dram/annotations Traceback (most recent call last): File "/scratch/st-ziels-1/psampara/dram_env/bin/DRAM.py", line 207, in args.func(**args_dict) File "/scratch/st-ziels-1/psampara/dram_env/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 1881, in merge_annotations_cmd merge_annotations(annotations_list, output_dir, write_annotations=True) File "/scratch/st-ziels-1/psampara/dram_env/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 1775, in merge_annotations all_annotations = pd.concat( File "/scratch/st-ziels-1/psampara/dram_env/lib/python3.10/site-packages/pandas/core/reshape/concat.py", line 372, in concat op = _Concatenator( File "/scratch/st-ziels-1/psampara/dram_env/lib/python3.10/site-packages/pandas/core/reshape/concat.py", line 429, in init raise ValueError("No objects to concatenate") ValueError: No objects to concatenate

It makes sense, since the directory was not exactly provided, so a search for the files within the annotation directories was not done.

3. So, I thought it might be the issue with finding individual files and copied all data within the individual parent annotation directories to a new directory. For example, I copied all files from the folder: "08_dram/annotations/annotation_bin.123" to a new folder "08_dram/annotations/all_files" with the parent directory name appended to the file name as such - "08_dram/annotations/all_files/bin.123_annotations.tsv". The "08_dram/annotations/all_files" folder now contains all annotations files for all bins.

Then I ran the program in this directory as such: DRAM.py merge_annotations -i 08_dram/annotations/all_files/* -o 08_dram/merge_anno

However, it also generated an error as following:

usage: DRAM.py [-h] {annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations} ... DRAM.py: error: unrecognized arguments: bin.112_annotate.log bin.112_annotations.tsv ... and so on, listing every file in the directory.

What is the correct syntax to run the "merge_annotations" program?

Thanks! Pranav

[psampara]

I figured out that I need to provide the input directory with quotes as such:

DRAM.py merge_annotations -i 'annotations/*' -o merge_anno