iMLP

The imlp cli tool predicts iMTS-L propensity profiles for proteins of interest.

General
Installation
Usage
Development

General

Installation

Dotnet tool

imlp is packaged as dotnet tool. To use it:

install the .NET SDK for your system
run either dotnet tool install imlp for a local or dotnet tool install -g imlp for a global installation
you can now run the tool via dotnet imlp ...

Dependencies on linux

The CNTK nuget package sadly only works ootb on windows. On linux, several native dependencies must be installed and be added to environment variables. The necessary libraries are the CNTK binaries themselves and OpenMPI.

the necessary cntk binaries can be downloaded here
for installation of OpenMPI, please follow this guide
finally, apply this fix:
- navigate to the location where you unpacked the cntk binaries
- run cp ./cntk/lib/Cntk.Core.CSBinding-2.7.so ./cntk/lib/libCntk.Core.CSBinding-2.7.dll

Docker

A Dockerfile can be downloaded under releases or found here. It takes care of setting up the necessary native dependencies of CNTK. Due to that, the resulting image will be quite large (~7GB). Build the dockerfile by running docker build . -t imlp

Published binaries

Download links to self-contained binaries can be found under releases. Linux users have to apply the same fixes as laid out under the dotnet tool section

Usage

USAGE: imlp [--help] [--sequence <sequence>] [--inputfile <inputFile>] [--outputfile <outputFile>] [--model <plant|nonplant>] [--plotdirectory <plotDirectory>] [--proteinheaderregex <proteinHeaderRegex>]
            [--verbosity <verbosity>]

OPTIONS:

    --sequence, -s <sequence>
                          A single, one-letter coded amino acid input sequence. Either --sequence (-s) 
                          or --inputFile (-f) must be specified.
    --inputfile, -f <inputFile>
                          Path to a fasta formatted input file that may contain multiple entries. Either 
                          --sequence (-s) or --inputFile (-f) must be specified.
    --outputfile, -o <outputFile>
                          (optional) Path to the desired output file, which will be tab separated (tsv). 
                          If not specified, output will be printed to stdout instead.
    --model, -m <plant|nonplant>
                          (optional) Model to use for prediction. Choose the one that is closest to your 
                          organism of interest: Either 'plant' or 'nonplant'. (default:nonplant)
    --plotdirectory, -p <plotDirectory>
                          (optional) Path to a directory to save plots to.
    --proteinheaderregex, -pr <proteinHeaderRegex>
                          (optional) Regular expression to extract protein names from fasta headers for 
                          the naming of plot output files. if not provided, plot files will be 'protein_{i}.html', 
                          where i is the index in the input.
    --verbosity, -v <verbosity>
                          (optional) The verbosity of the logging process. 0(Silent) | 1(Error) | 2(Warn) | 3(Info) 
                          | >=4 : Debug | (default:1)
    --help                display this list of options.

ZimmerD / iMLP-1