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##
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## PhosMHCpred is a predictor for HLA-I - phosphorylated ligand interactions.
##
## CITATION:
## If you use PhosMHCpred in a publication, please cite:
## Solleder et al., MCP (2020).
##
## FOR-PROFIT USERS:
## If you plan to use PhosMHCpred or any data provided with the script in any for-profit
## application, you are required to obtain a separate  license. To do so, please contact
## [email protected] or [email protected] at the Ludwig Institute for  Cancer Research Ltd.
##
## CONTACT:
## Marthe Solleder ([email protected]) and David Gfeller ([email protected]).
##
##
######



## PRELIMINARY

  Open the PhosMHCpred.py file and replace path (l. 35) by the path to the PhosMHCpred/ directory.



## COMMAND

  ./PhosMHCpred.py -p peptides -a alleles [-o output]
  
  To test PhosMHCpred: ./PhosMHCpred.py -p ./test/testPeptides.txt -a ./test/testAlleles.txt -o ./test/results.txt 
  or: ./PhosMHCpred.py -p ./test/testPeptides.txt -a HLA-A0201,HLA-B4002 -o ./test/results.txt 


peptides [required]:
  File listing all the peptides or give a list of peptides in the command line separated by a single
  comma "," (e.g. ALLSRNHsL,FLIsKVEQI,GLYNsTDSL).

alleles [required]:
  Define HLA-I allele for prediction (give as HLA-A0101). If predictions with more than one alleles
  are performed, give a file listing the alleles or list the alleles separated by a single 
  comma (e.g. -a HLA-A0201,HLA-B4002).

output [optional]:
  Give a name of the output file (if non given, results are saved as "results.txt" in current directory).



## OTHER INFORMATION

- PhosMHCpred is trained on naturally presented phosphorylated and unmodified HLA-I ligands and gives
  a score for different peptides to identify the most likely HLA-I ligands for an allele (but does not
  predict affinity values). 

- The predictor can be run with more than one allele. In this case, the predictions are carried out
  for each allele separately and the predictor outputs independent results for the alleles.

- The results are provided in [output]/results.txt