awkbioinformaticsfasta

Replacing fasta header without key-value pair file

I am trying the following to replace fasta headers without key-value pairs using bioawk

for infile in $(ls *.faa)
do
        prefix=$(basename $infile .faa)
        bioawk -c fastx '{ print ">"$prefix"_" ++i "\n"$seq }' < ${infile} > ${prefix}_hdrrn.faa
done

Basically, I want to change the headers in my species_name.faa file to

>species_name_1
>species_name_2
...
>species_name_n

The problem is the $prefix inside bioawk print is not working. The error I get is:

bioawk: illegal field $(), name "prefix" input record number 1, file source line number 1

Why the substitution is not happening?

Solution

  • It was too easy with seqkit. using 'nr' does the trick !

    for infile in $(ls *.faa)
do
    prefix=$(basename $infile .faa)
    echo "prefix is ${prefix}"
    seqkit replace -p .+ -r ${prefix}_{nr} --nr-width 4 $infile -o ${prefix}_hdrrn.faa
done
echo "done"