5HT_pain_ephys_source/rename_ephys.sh

#!/bin/bash

#------------------------------------------------------------------------------#

source_folder=`pwd`
target_folder=`pwd`

cells="A B C D E F G H I J K L"

runs=`seq 1 4`

subjects=`seq 56 308`

## Files
for i_subject in $subjects
do

    echo "\n\nProcessing subject ${i_subject}"

    sub_folder=$source_folder/sub-${i_subject}/ephys

    for i_cell in $cells
    do

        file=`ls ${sub_folder}/*.smr | grep ${i_cell}*.smr`

        if [ -z "$file" ]
        then
            echo "no file: ${i_subject}*${i_cell}*.smr"

        else
            echo " Processing cell ${i_cell}"

            for i_run in $runs
            do

                smr_file=`ls ${sub_folder}/*.smr | grep ${i_cell}${i_run}.smr`   
                
                if [ -z "$smr_file" ]
                then
                    echo "no file: ${i_subject}*${i_cell}${i_run}.smr"

                else
                    echo "  processing run ${i_run}"

                    target_name=sub-${i_subject}_sample-${i_cell}_run-${i_run}_ephys.smr
                    echo $smr_file "-->" $sub_folder/$target_name
                    mv -v $smr_file $sub_folder/${target_name}

                    S2R_file=`echo $smr_file | sed s@smr@S2R@g`
                    target_name=`echo $target_name | sed s@smr@S2R@g`
                    echo $S2R_file "-->" $sub_folder/$target_name
                    mv -v $S2R_file $sub_folder/${target_name}

                fi

            done        

        fi   

    done

    # # if spreadhsheet data we process that subject
    # xls_files=$source_folder/${i_subject}.xls
    # xls_files=`find $xls_files`

    # if [ -z "$xls_files" ]
    # then
    #     echo "no file: ${i_subject}.xls: skipping subject"

    # else

    #     echo "processing subject ${i_subject}"

    #     subject_folder=$target_folder/sub-${i_subject}
    #     target_name=sub-${i_subject}_scans.xls

    #     # mkdir -p $subject_folder/ephys

    #     # mv -v $xls_files $subject_folder/$target_name


    #     done
    # fi    

done