# Some examples of usage of computeRT and computePI

# Path for InSilicoSpectro folder
INSILICOSPECTRO=$HOME/InSilicoSpectro
# Path for InSilico library
INSILICO=$INSILICOSPECTRO/lib/InSilicoSpectro/InSilico

# Getting some help
$INSILICO/computeRT.pl --help
$INSILICO/computePI.pl --help
$INSILICO/computeRT.pl --man
$INSILICO/computePI.pl --man

# Compute retention time for peptides in file data/test1 by Hodges method
$INSILICO/computeRT.pl --method=Hodges --current=Guo86 data/test1
# Compute isoelectric point by iterative method
$INSILICO/computePI.pl --method=iterative --current=Lehninger data/test1

# Perform a pipeline
$INSILICO/computeRT.pl --method=Hodges data/test1 |$INSILICO/computePI.pl --method=iterative -

# Compute isoelectric point using parameters saved in data/param.xml and calibrate using data/expdata
$INSILICO/computePI.pl --method=iterative --readparam=data/paramPI.xml --calibratefrom=data/expdata data/test1 data/test2

# Learn coefficientes for Hodges method, compute retention time from stdin and save params 
$INSILICO/computeRT.pl --method=Hodges --learnfrom=data/expdata --saveparam=data/paramRT.xml -
# Give additional settings in data/sethod.xml
$INSILICO/computeRT.pl --method=Hodges --learnfrom=data/expdata --settings=data/sethod.xml --saveparam=data/paramRT.xml -

# Save output data in data/results
$INSILICO/computeRT.pl --method=Petritis --learnfrom=data/expdata --out=data/results data/test2




