Shell Programming and Scripting

S1_L3_all_R1.fastq
S1_L3_all_R2.fastq
S1_L4_all_R1.fastq
S1_L4_all_R2.fastq
.
.
S1_L8_all_R1.fastq
S1_L8_all_R1.fastq

S1_L3_all_R1.fasta
S1_L3_all_R2.fasta
.
.
S1_L8_all_R1.fasta
S1_L8_all_R2.fasta

for((n=3;n<=8;n++))
do 
for((k=1;k<=2;k++))
do 
for f  in S1_L$n_all_filt_R*.fastq
do 
echo $f
cat $f | perl -e my file processing > S1_L$n_all_filt_R$k.fasta
done
done
done

$ n_=1234
$ echo $n_

1234

$

for((n=3;n<=8;n++))
do 
        for((k=1;k<=2;k++))
        do 
                for f  in S1_L${n}_all_filt_R*.fastq
                do 
                        echo $f
                        perl -e my file processing <"$f" > S1_L${n}_all_filt_R${k}.fasta
                done
        done
done

for n in 3 4 5 6 7 8
do
        for k in 1 2
        do
        ...
        done
done

# This entire loop of code will have 'filename' as its standard input
while read LINE
do
...
done <filename

# This entire subshell will read from 'filename' as its standard input and write to 'outfile' as its standard output
# 'read' will read the first line.  Then 'echo' will write 'something' into 'outfile'.
# Then 'grep' will hunt for 'word' in the rest of the file and print any results after 'something' in 'outfile'.
( read FIRSTLINE ; echo "something" ; grep "word" ) <filename >outfile