### make whole human spectral library from MS-Fragger output pepxml
C:\TPP\bin\spectrast.exe -M spectrast.usermods -c_BIN! -c_RDYrev_ -cP0.9716 -cIHCD -cNC:\Users\jymbc\Desktop\293library\T293 C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_30.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_40.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_45.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_50.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_55.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_60.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_65.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_70.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_75.pep.xml C:\Users\jymbc\Desktop\library\libraryfiles\interact-T293library_80.pep.xml
### get consensus
C:\TPP\bin\spectrast.exe -M spectrast.usermods -cAC -c_BIN! -cIHCD -cNC:\Users\jymbc\Desktop\293library\T293_consensus C:\Users\jymbc\Desktop\293library\T293.splib

## add decoys
C:\TPP\bin\spectrast.exe -M spectrast.usermods -cAD -cc -c_BIN! -cIHCD -cNC:\Users\jymbc\Desktop\293library\T293_decoys C:\Users\jymbc\Desktop\293library\T293_consensus.splib

## convert to tsv
conda activate venv_lib
python C:\Users\jymbc\Desktop\spectrast2tsv.py -m C:\Users\jymbc\Desktop\spectrast.usermods -g -17.03,-18.01 -l 300,2000 -s b,y -x 1,2 -o 3 -n 20 -p 0.05 -d -e -k openswath -a C:\Users\jymbc\Desktop\293library\T293_highres_decoys.tsv C:\Users\jymbc\Desktop\293library\T293_decoys.splib