commandline_tutorial.rst

Using MHCflurry from the command-line
=====================================


mhcflurry-predict
-----------------

The ``mhcflurry-predict`` command generates predictions from the command-line.

.. code:: shell

    $ mhcflurry-predict --alleles HLA-A0201 HLA-A0301 --peptides SIINFEKL SIINFEKD SIINFEKQ
    allele,peptide,mhcflurry_prediction,mhcflurry_prediction_low,mhcflurry_prediction_high
    HLA-A0201,SIINFEKL,5326.541919062165,3757.86675352994,7461.37693353508
    HLA-A0201,SIINFEKD,18763.70298522213,13140.82000240037,23269.82139560844
    HLA-A0201,SIINFEKQ,18620.10057358322,13096.425874678192,23223.148184869413
    HLA-A0301,SIINFEKL,24481.726678691946,21035.52779725433,27245.371837497867
    HLA-A0301,SIINFEKD,24687.529360239587,21582.590014592537,27749.39869616437
    HLA-A0301,SIINFEKQ,25923.062203902562,23522.5793450799,28079.456657427705

The predictions returned are affinities (KD) in nM. The ``prediction_low`` and
``prediction_high`` fields give the 5-95 percentile predictions across
the models in the ensemble. The predictions above were generated with MHCflurry
0.9.2.

Your exact predictions may vary slightly from these (up to about 1 nM) depending
on the Keras backend in use and other numerical details. Different versions of
MHCflurry can of course give results considerably different from these.

You can also specify the input and output as CSV files. Run
``mhcflurry-predict -h`` for details.