Shell Programming and Scripting

# select file
printf "please select a file to analyze with entered gene or genes  \n"
select file in $(cd /home/cmccabe/Desktop/NGS/API/test/bedtools;ls);do break;done
            echo $file "will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for vizulization, and calculate 20x and 30x coverage for the entered gene(s)"
logfile=/home/cmccabe/Desktop/NGS/API/test/process.log
for file in /home/cmccabe/Desktop/NGS/API/test/bedtools/$file; do
     echo "Start selcted file creation: Panel: ${FUNCNAME[0]} Date: $(date) - File: $file"
     bname=$(basename $file)
     pref=${bname%%.txt}
     while read -r file; do mv "$file" /home/cmccabe/Desktop/NGS/panels/reads/${pref}_OTHER.txt ; done
     echo "End selected file creation: $(date) - File: $file"
done >> "$logfile"

file1.txt
file2.txt
file3.txt

# select file
printf "please select a file to analyze with entered gene or genes  \n"
select file in $(cd /home/cmccabe/Desktop/NGS/API/test/bedtools;ls);do break;done
            echo $file "will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for vizulization, and calculate 20x and 30x coverage for the entered gene(s)"
logfile=/home/cmccabe/Desktop/NGS/API/test/process.log
for file in /home/cmccabe/Desktop/NGS/API/test/bedtools/$file; do
     echo "Start selcted file creation: Date: $(date) - File: $file"
     bname=$(basename $file)
     pref=${bname%%.txt}
     mv "$file" /home/cmccabe/Desktop/NGS/panels/reads/${pref}_OTHER.txt
     echo "End selected file creation: $(date) - File: $file"
done >> "$logfile"

file1.txt will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for visualization, and calculate 20x and 30x coverage for the entered gene(s)
mv: cannot move ‘/home/cmccabe/Desktop/NGS/API/test/bedtools/file1.txt’ to ‘/home/cmccabe/Desktop/NGS/panels/reads/file1_OTHER.txt’: No such file or directory

set -vx # for debugging only
SRC_DIR=/path/to/source_dir/
DEST_DIR=/path/to/destination_dir/ # notice the ending / and the upper case detonating that it is a constant that will not change in the live of the script.
# if you can not guarantee the correct permissions to access and modify the source and destination this might fail.

select filename in "$SRC_DIR"*; do
    # The -v is to display what it is done
    mv -v "$filename" "$DEST_DIR"
    break
done

PS3="please select a file to analyze with entered gene or genes (or 1 or q to quit): "
select ANSW in  exit /mnt/9/playground/*
                    do  case $REPLY in 1|[eq]*) break;; esac
                        echo $ANSW "will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for vizulization, and calcul
                        echo "Start selected file creation: Panel: ${FUNCNAME[0]} Date: $(date) - File: $ANSW"
                        file=${ANSW##*/}
                        echo mv -v "$ANSW" /mnt/9/playground/LA/${file%.jpg}_OTHER.txt ;    
                        echo "End selected file creation: $(date) - File: $ANSW"
                    done | tee LOG