Prep.sh

#!/bin/bash

DIR_IN="/home/nas151/WORKING_DATA/DNA_Sequencing/Preprocessing/Bill/2015_05/"
DIR_OUT="/home/nas151/WORKING_DATA/DNA_Sequencing/Preprocessing/Bill/2015_05/"
SAMPLES_IN=`ls ${DIR_IN}/*R1*`

for i in $SAMPLES_IN
do
  # echo $i
  SAMPLE_BASE=`basename $i`
  FILE_OUT_R1=$(echo $SAMPLE_BASE | sed 's/L001_R1/R1/g')
  FILE_OUT_R2=$(echo $SAMPLE_BASE | sed 's/L001_R1/R2/g')
  SAMPLE_ID=$(echo $FILE_OUT_R1 | sed 's/_R1.fastq.gz//g')
  echo $SAMPLE_ID

  # touch ${DIR_OUT}/${FILE_OUT_R1}
  # touch ${DIR_OUT}/${FILE_OUT_R2}
  #
  # for j in ${DIR_IN}/${SAMPLE_ID}*R1*
  # do
  #   echo $j
  #   zcat $j >> ${DIR_OUT}/${FILE_OUT_R1}
  # done
  #
  # for j in ${DIR_IN}/${SAMPLE_ID}*R2*
  # do
  #   echo $j
  #   zcat $j >> ${DIR_OUT}/${FILE_OUT_R2}
  # done

  mkdir -p ${DIR_OUT}/Sample_${SAMPLE_ID}/Raw_Data/
  mv ${DIR_OUT}/${SAMPLE_ID}* ${DIR_OUT}/Sample_${SAMPLE_ID}/Raw_Data/

done