Shell Programming and Scripting

awk: cmd. line:2: fatal: cannot open file `C:/path/to/file/.txt
.hg19_multianno.txt' for reading (No such file or directory)

for f in C:/path/to/file/${id}.txt.hg19_multianno.txt ; do
     bname=`basename $f`
     pref=${bname%%$.*.txt}
     awk -v F=49 -v T=96 '
BEGIN{FS=OFS="\t"}
{ b=T+1
t=T<NF?T:NF
for(i=F;i<NF-t+F;i++) $i=$(b++)
NF=--i}1' $f > C:/path/to/file/${pref}_dbremoved.txt
done

1234_dbremoved

1234.txt
5678.txt
9123.txt

dir_path=$PWD
while IFS= read line
do
    id=${line%.*}
    echo "$dir_path/${id}.whatever_else"
done < list

# read id from target.txt
dir_path=C:/Users/cmccabe/Desktop/annovar
while IFS= read line
do
    id=${line%.*}
    echo "$dir_path/${id}.hg19_multianno.txt"
done < target.txt

# remove -dbnsfp33a fields 49-96 from multianno
${id}=(line)
for f in 'C:\Users\cmccabe\Desktop\annovar\${id}.txt.hg19_multianno.txt' ; do
     bname=`basename $f`
     pref=${bname%%$.*.txt}
     awk -v F=49 -v T=96 '
BEGIN{FS=OFS="\t"}
{ b=T+1
t=T<NF?T:NF
for(i=F;i<NF-t+F;i++) $i=$(b++)
NF=--i}1' $f > C:/Users/cmccabe/Desktop/annovar/${pref}_dbremoved.txt
done

dir_path=C:/Users/cmccabe/Desktop/annovar
while IFS= read line
do
    id=${line%.*}
    awk -v F=49 -v T=96 '
        BEGIN{ FS=OFS="\t" }
        { b=T+1
           t=T<NF?T:NF
           for(i=F;i<NF-t+F;i++) {
              $i=$(b++)
              NF=--i}
         }1' "$dir_path/${id}.hg19_multianno.txt" > "$dir_path/${id}_dbremoved.txt"
done < target.txt