Perform a PEFF test under Linux #### Check $HOME and set the location of the Proteomics::PEFF distribution cd $HOME set PEFF=$HOME/ProteomicsPEFF mkdir $PEFF cd $PEFF wget http://www.peptideatlas.org/export/PEFF/ProteomicsPEFF.zip unzip ProteomicsPEFF.zip #### If okay, add the bin area to the PATH and set the testData location set PATH=$PEFF/bin/PEFF;$PATH set PEFFTEST=$PEFF/testData/PEFF #### Test the configuration. If this doesn't work, troubleshoot before proceeding perl $PEFF/bin/testConfig.pl #### Test the validator on some files. The first 3 should produce no errors. #### The fourth should spew lots of errors because the file is NOT valid validatePEFF --input $PEFFTEST/PEFF_Minimal_Valid.peff validatePEFF --input $PEFFTEST/PEFF_AnnotID_Insulin_Valid.peff validatePEFF --input $PEFFTEST/crap.peff validatePEFF --input $PEFFTEST/PEFF_Tiny_INValid1.peff #### In a test directory, create a PEFF file from crap.fasta, applying (di+)methyl to TRYP lysines cd $HOME mkdir testPEFF cd testPEFF copy $PEFFTEST/crap.fasta . copy $PEFFTEST/crap.fasta.header . copy $PEFFTEST/crap_alterations.txt . alterPEFF --operation convertFASTAToPEFF --input crap.fasta --output crap.peff --databaseMetadataFile crap.fasta.header --alterations crap_alterations.txt --verbose 1