3 cd /share
/FGI2017B
/users
/huxs
/gsj20200911
7 (($#)) ||
return 1 # At least delimiter required
8 local -- delim
="$1" str IFS
=
10 str
="${*/#/$delim}" # Expand arguments with prefixed delimiter (Empty IFS)
11 echo "${str:${#delim}}" # Echo without first delimiter
15 IFS
=$
'\n' INFILEC
=( `cat "cRNA.lst"`)
17 #echo "${INFILEC[0]} $cntF"
18 for (( i
= 0 ; i
< ${#INFILEC[@]} ; i
++ )); do
20 IFS
=$
'\t' read -ra INDAT
<<<"${INFILEC[$i]}";
21 IFS
=' ,' read -ra GROUPA
<<<"${INDAT[1]}";
22 IFS
=' ,' read -ra GROUPB
<<<"${INDAT[2]}";
25 echo "$i ${INDAT[0]} $cntA:[${GROUPA[@]}] - $cntB:[${GROUPB[@]}].";
26 for (( x
= 0 ; x
< cntA
; x
++ )); do
27 FGROUPA
[$x]="alnSTAT/${GROUPA[$x]}Aligned.sortedByCoord.out.bam";
29 for (( y
= 0 ; y
< cntB
; y
++ )); do
30 FGROUPB
[$y]="alnSTAT/${GROUPB[$y]}Aligned.sortedByCoord.out.bam";
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[@]}";