Running neuripp

[soosum]

Hi,

I have recently installed neuripp and tried to have a test run. However, I'm seeing messages like this (see below) on the help page.

/home/susan/Programs/neuripp-master/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/home/susan/Programs/neuripp-master/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
usage: classify.py [-h] -m
{cnn-parallel,cnn-linear,cnn-linear-lstm,cnn-parallel-lstm,lstm}
[-w WEIGHTS] [-outname OUTNAME] [-outdir OUTDIR]
[--keep_negatives] [-b BATCH_SIZE] -i INPUT

optional arguments:
-h, --help show this help message and exit
-m {cnn-parallel,cnn-linear,cnn-linear-lstm,cnn-parallel-lstm,lstm}, --model {cnn-parallel,cnn-linear,cnn-linear-lstm,cnn-parallel-lstm,lstm}
Model Architecture (default: cnn-parallel)
-w WEIGHTS, --weights WEIGHTS
Weights File for Model (default: None)
-outname OUTNAME Prefix for Positive or Negative Data (default:
peptide)
-outdir OUTDIR Path to Output Directory (default:
/home/susan/Programs/neuripp-master)
--keep_negatives Also output a fasta file with the negative peptides
(default: False)
-b BATCH_SIZE, --batch_size BATCH_SIZE
Number of Samples to Give Model at a Time (default:
1000)
-i INPUT, --input INPUT
Fasta File Containing Sequences to Classify (default:
None)

Could you please advice? Thanks.

[emzodls]

I don't think it's an error, just a warning that some function being called is going to be deprecated in the future. Did you specify an input fasta file with the flag -i ?

[soosum]

Yes, I activated the virtual environment for neuripp and tried to run using the command "python classify.py -w /path/to/weight -i test.fasta", however it refuse to take my fasta file.

[emzodls]

are you using "-w /path/to/weight"? You have to replace this with the actual path to the weights on your computer (they're in the weights folder) choose the right set of weights for your specified model.

[soosum]

No, I have replaced them with my directory here.

[soosum]

Anyway, I got it running now by specifying "--keep_negatives -m lstm -w /path/to/weights/"

[YQXue]

This is probably the problem of tensorflow, I also run into this problem. And to fix this problem, you may need to download a proper version of tensorflow or update your current one~