READMEspotdis

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Hello user,
Thank you for your interest in our predictor. SPOT-DISORDER-SINGLE requires 
several python packages, please verify that they are installed before use:

    tensorflow (v1.4)    ---> see https://www.tensorflow.org/install/
    numpy
    tqdm
    pickle

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USAGE:
SPOT-DISORDER2-SINGLE requires no external predictors and should read your input 
fasta/sequence files. 

To run for a sample protein, please locate the target protein's fasta or 
sequence file and run:

    ./run_spotdis_single.py /path/to/fasta/or/seq.seq

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EXTRA OPTIONS:
There are several options that this predictor supports:

    "--gpu 0"           use this command to utilise the GPU for testing. This 
                        is set to -1 by default 
    "--batch_size 10"   use this command to set the batch size for testing. For   
                        datasets using larger proteins, reduce this number if 
                        you encounter memory issues.
    "--quiet 1"         use this command to silence the output
    "--output_dir '/put/outputs/here/'" 
                        use this command to set the output 
                        directory to another directory other than where the 
                        input file is located

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EXAMPLES:
Another example, for running on an example protein directory:

./run_spotdis_single.py --gpu 0 --batch_size 50 --quiet 1 --output_dir "/put/here/" /fasta/directory*fasta
 
or without any options

    ./run_spotdis_single.py /fasta/directory*fasta

This will run over all fasta files in the directory /fasta/directory.

For running over a text list of file locations, use this:

    ./run_spotdis_single.py `cat /list/of/fasta/locations`

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PLEASE CITE!:
If you use this predictor in your research, please cite:

Hanson, J., Paliwal, K., and Zhou, Y., Accurate Sequence-Based Prediction of Protein Disorder by an Ensemble of Deep Recurrent Architectures, 2018

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Thanks again!
Jack Hanson and the Sparkslab team