The imlp cli tool predicts iMTS-L propensity profiles for proteins of interest.
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 ordotnet tool install -g imlp
for a global installation - you can now run the tool via
dotnet imlp ...
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
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
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: 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.