csparc2rel

#!/bin/bash

# Test to make sure csparc2star.py is in PATH and installed correctly:
csparc2star.py -h &> /dev/null
if [ $? -ne 0 ]; then
        echo Failed to run csparc2star.py. Are you in the correct virtual environment? Did you check your path?
        exit
fi

# Change this to your csparc scratch directory. This should be where all your P* dirs are
CSPARC_DIR="/path/to/your/cryosparc/projects"
echo Using cryosparc dir $CSPARC_DIR
echo If that looks wrong, modify the script at line 11

read -p "What cryosparc project are you converting? Number only: " PROJECT
PROJECT=P${PROJECT}
read -p "What is the job number of the refinement? Number only: " REFINE
REFINE=J${REFINE}

# figure out extract job's number
pushd $CSPARC_DIR/$PROJECT/exports/jobs/${PROJECT}_$REFINE*/*particles/ > /dev/null
EXTRACT=$(ls * | grep extract -B 1 | grep -o J[0-9]*)
popd > /dev/null


echo Now converting ${PROJECT} ${REFINE} to a RELION project...

mkdir -p ${EXTRACT}/extract
pushd ${EXTRACT}/extract > /dev/null
ln -s ${CSPARC_DIR}/${PROJECT}/${EXTRACT}/extract/*.mrc -t .

echo Done linking images...

# depending on which `rename` you have installed, you may
# need to use the one I've commented out here, instead of the
# one I use.
#
# rename .mrc .mrcs *.mrc
rename s/.mrc/.mrcs/g *.mrc

echo "Done renaming images. If you saw an error, go change the rename command (line 39)."
echo Converting coordinates...

# swapxy and inverty are important for keeping micrograph coordinates correct between the two
# packages. But if you get errors about particles being outside the micrograph, try removing
# those options

popd > /dev/null
csparc2star.py $(ls ${CSPARC_DIR}/${PROJECT}/${REFINE}/cryosparc*particles.cs | tail -n 1) from_csparc.star --swapxy --inverty
echo .star file created
sed -i 's/particles.mrc/particles.mrcs/g' from_csparc.star
sed -i 's/>//g' from_csparc.star

echo .star file fixed
echo "done :)"

For this to work, the job must be exported (in the cryoSPARC web interface, it's one of the job actions)