Question

I used the following code to extract protein residues from text files.

awk '{
if (FNR == 1 ) print ">" FILENAME  
if ($5 == 1 && $4 > 30) {
printf $3
 }
}
END { printf "\n"}'  protein/*.txt > seq.txt

I got the following output when I used the above code.

>1abd
MDEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR>1axc
RQTSMTDFYHSKRRLIFS>1bxc
RQTSMTDFYHSKRRLIFSPRR>1axF
RQTSMTDFYHSKRR>1qqt
ARPYQGVRVKEPVKELLRRKRG

I would like to get the output as shown below.How do I change the above code to get the following output?

>1abd
MDEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR
>1axc
RQTSMTDFYHSKRRLIFS
>1bxc
RQTSMTDFYHSKRRLIFSPRR
>1axF
RQTSMTDFYHSKRR 
>1qqt
ARPYQGVRVKEPVKELLRRKRG

Answer 1

This might work for you:

awk '{
if (FNR == 1 ) print newline ">" FILENAME  
    if ($5 == 1 && $4 > 30) {
        newline="\n";
        printf $3
    }
}
END { printf "\n"}'  protein/*.txt > seq.txt