UNIX for Beginners Questions & Answers

set -x
DIR=/home/cmccabe/Desktop/f1   ## define data directory path
for RDIR in "$DIR"/R_2019* ; do
      BAM=$(find "$RDIR"/bam -type f -name "*.bam" -printf '%P\n')
       SAMPLE=$(echo $BAM|cut -d. -f1)
echo "$SAMPLE"
done

R_2019_03_12_11_10_20_user_S5-0271-99
     -bam
       19-0000-LastName-FirstName.bam.bai 19-0000-LastName-FirstName.bam 19-0001-Las-Fir.bam.bai 19-0001-Las-Fir.bam 190319-Control.bam.bai 190319-Control.bam
R_2019_03_12_13_59_54_user_S5-0271-100
     -bam
        19-0004-La-Fi.bam.bai 19-0004-La-Fi.bam.bam 19-0005-Last-Firs.bam.bai 19-0005-Last-Firs.bam 19-0008-LastN-FirstN.bam.bai 19-0008-LastN-FirstN.bam 190320-Control.bam.bai 190320-Control.bam

set -x
cmccabe@DTV-A5211QLM:~$ DIR=/home/cmccabe/Desktop/f1   ## define data directory path
+ DIR=/home/cmccabe/Desktop/f1
cmccabe@DTV-A5211QLM:~$ for RDIR in "$DIR"/R_2019* ; do
>       BAM=$(find "$RDIR"/bam -type f -name "*.bam" -printf '%P\n')
>        SAMPLE=$(echo $BAM|cut -d. -f1)
> echo "$SAMPLE"
> done
+ for RDIR in '"$DIR"/R_2019*'
++ find /home/cmccabe/Desktop/f1/R_2019_03_12_11_10_20_user_S5-0271-99/bam -type f -name '*.bam' -printf '%P\n'
+ BAM='190319-Control.bam
19-0001-Las-Fir.bam
19-0000-LastName-FirstName.bam'
++ echo 190319-Control.bam 19-0001-Las-Fir.bam 19-0000-LastName-FirstName.bam
++ cut -d. -f1
+ SAMPLE=190319-Control
+ echo 190319-Control
190319-Control
+ for RDIR in '"$DIR"/R_2019*'
++ find /home/cmccabe/Desktop/f1/R_2019_03_12_13_59_54_user_S5-0271-100/bam -type f -name '*.bam' -printf '%P\n'
+ BAM='190320-Control.bam
19-0008-LastN-FirstN.bam
19-0005-Last-Firs.bam
19-0004-La-Fi.bam'
++ echo 190320-Control.bam 19-0008-LastN-FirstN.bam 19-0005-Last-Firs.bam 19-0004-La-Fi.bam
++ cut -d. -f1
+ SAMPLE=190320-Control
+ echo 190320-Control
190320-Control

# -------------- new inner loop
     find "$RDIR"/bam -type f -name "*.bam" -printf '%P\n' |
    while read BAM
    do
       SAMPLE=$(echo $BAM|cut -d. -f1)  #  lose the cut and use this instead: SAMPLE=${BAM%%.*}  
      #   Try it first before running in a script
      # do things with $SAMPLE here  I guess:  like mv $BAM $SAMPLE
   done
# ---------- end new inner loop

for RDIR in "$DIR"/R_2019* ; do
     find "$RDIR"/bam -type f -name "*.bam" -exec /path/to/movescript.sh {} \;
done

!# /bin/sh

echo mv "${1}" "${1%.bam}"

exit $?