gaarangoa / deeparg2.0

deepARG using deep semantic representation

DNN-ARG plus v2.0

This is an experimental model. This repository is not deeparg, please use deeparg repository at https://github.com/gaarangoa/deeparg

deeparg2.0's Issues

the number of threads and the output

Hi,

I am using the software to find the ARGs and calculate the abundance. However, I have some questions:

1. Is there any parameter to limit the threads? It seems that when runing the diamond in the short_reads_pipiline, it will occupy all the threads.

2. Is there any parameter to minimize the results? I think there were many file useless in the downstream analyses.

can't install with docker

when I tried to install deeparg with docker build, i failed at step 2
Step 2/7 : ADD ./src /dplus/src
ADD failed: file not found in build context or excluded by .dockerignore: stat src: file does not exist

Repetitive ARG category names in the output?

Hi thanks for the amazing tool! I found myself a bit puzzled about the ARG category names in the output file. Would like to seek your idea about it.

I have attached the screenshot as an example. Some ARG category entries seemed repetitive. And sometimes, there is a "/" separating some ARG categories, but sometimes it is a "," separating ARG categories. Do they mean different things? Would be grateful for your comments in understanding them! Are these resulted from the correction of gene annotations used in different ARG databases (CARD, ARDB, and UNIPROT)? If yes, what would the difference be between "/", ",", and ":" symbols? And what would your suggestions be in dealing with these entries?

Much appreciated!
Elly

Installation error

Hello There,

I am trying to use deeparg download_data -o ./ command

it throws error of HTTPconnection error

conda support

Hi, Arango,

There is any plan to support deeparg which can be installed using conda?

Thanks,
Jie

issue with pip install: deepargs predict bug

I built a conda env with the following commands:

conda create -n deeparg_env python=2.7.18 
conda activate deeparg_env 
conda install -c bioconda diamond==0.9.24 
pip install deeparg==1.0.2 
deeparg download_data -o /path/to/local/directory/ 

I try to run deeparg predict -i sim_dat/fasta/contigs.fasta -o deeparg_out_combo_fasta --model SS and get the following error:

/home/ewissel/miniconda3/envs/deeparg_env/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/home/ewissel/miniconda3/envs/deeparg_env/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
INFO:root:DIAMOND blastx alignment
Traceback (most recent call last):
  File "/home/ewissel/miniconda3/envs/deeparg_env/bin/deeparg", line 8, in <module>
    sys.exit(main())
  File "/home/ewissel/miniconda3/envs/deeparg_env/lib/python2.7/site-packages/deeparg/entry.py", line 184, in main
    args.func(args)
  File "/home/ewissel/miniconda3/envs/deeparg_env/lib/python2.7/site-packages/deeparg/entry.py", line 36, in predict
    '-d', args.data_path+"/database/"+args.model_version+"/features",
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

This seems to be a bug with the pip install of deepargs. Let me know if this package is actively maintained and if you plan to fix this soon!

deeparg installation

Hello I was trying to isntall deeparg using pip recipe pip install deeparg==1.0.2 but pip cannot find the package.

Also I tried installing it bi following the installation guide provieded here: https://bench.cs.vt.edu/deeparg which is performed by cloning the source code but I cannot find the "options.py" file that is mentioned on the guide.

Finally I tried copying the repository (https://github.com/gaarangoa/deeparg2.0.git) , but the provided README files doesnt provide a installation guide.

So how can I install the program?

thanks for your time.