R/deseq2/2rna.sh

   1 #!/bin/bash
   2
   3 cd /share/FGI2017B/users/huxs/gsj20200911
   4 mkdir -p fcSTARg
   5
   6 array::join() {
   7   (($#)) || return 1 # At least delimiter required
   8   local -- delim="$1" str IFS=
   9   shift
  10   str="${*/#/$delim}" # Expand arguments with prefixed delimiter (Empty IFS)
  11   echo "${str:${#delim}}" # Echo without first delimiter
  12 }
  13
  14 declare -a INFILEC
  15 IFS=$'\n' INFILEC=( `cat "cRNA.lst"`)
  16 #cntF=${#INFILEC[@]}
  17 #echo "${INFILEC[0]} $cntF"
  18 for (( i = 0 ; i < ${#INFILEC[@]} ; i++ )); do
  19         declare -a INDAT;
  20         IFS=$'\t' read -ra INDAT <<<"${INFILEC[$i]}";
  21         IFS=' ,' read -ra GROUPA <<<"${INDAT[1]}";
  22         IFS=' ,' read -ra GROUPB <<<"${INDAT[2]}";
  23         cntA=${#GROUPA[@]};
  24         cntB=${#GROUPB[@]};
  25         echo "$i ${INDAT[0]} $cntA:[${GROUPA[@]}] - $cntB:[${GROUPB[@]}].";
  26         for (( x = 0 ; x < cntA ; x++ )); do
  27                 FGROUPA[$x]="alnSTAT/${GROUPA[$x]}Aligned.sortedByCoord.out.bam";
  28         done;
  29         for (( y = 0 ; y < cntB ; y++ )); do
  30                 FGROUPB[$y]="alnSTAT/${GROUPB[$y]}Aligned.sortedByCoord.out.bam";
  31         done;
  32         #strA=`array::join ' ' ${FGROUPA[@]}`;
  33         #strB=`array::join ' ' ${FGROUPB[@]}`;
  34         theCmd="featureCounts -a gencode.v35.primary_assembly.annotation.gtf -o fcSTARg/${INDAT[0]}.txt -T 48 -t exon -g gene_id ${FGROUPA[@]} ${FGROUPB[@]}";
  35         #echo "$i $theCmd";
  36         bash -c "$theCmd";
  37         unset FGROUPA;
  38         unset FGROUPB;
  39 done