How to rename fasta header based on filename in multiple files?-CodePudding

I have a directory with multiple fasta file named as followed:

BC-1_bin_1_genes.faa
BC-1_bin_2_genes.faa
BC-1_bin_3_genes.faa
BC-1_bin_4_genes.faa

etc. (about 200 individual files)

The fasta header look like this:

>BC-1_k127_3926653_6 # 4457 # 5341 # -1 # ID=2_6;partial=01;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.697

I now want to add the filename to the header since I want to annotate the sequences for each file.I tried the following:

for file in *.faa;
   do
       sed -i "s/>.*/${file%%.*}/" "$file" ;
done

It worked partially but it removed the ">" from the header which is essential for the fasta file. I tried to modify the "${file%%.*}" part to keep the carrot but it always called me out on bad substitutions.

I also tried this:

awk '/>/{sub(">","&"FILENAME"_");sub(/\.faa/,x)}1' *.faa

This worked in theory but only printed everything on my terminal rather than changing it in the respective files.

Could someone assist with this?

CodePudding user response：

It's not clear whether you want to replace the earlier header, or add to it. Both scenarios are easy to do. Don't replace text you don't want to replace.

for file in ./*.faa;
do
    sed -i "s/^>.*/>${file%%.*}/" "$file"
done

will replace the header, but include a leading > in the replacement, effectively preserving it; and

for file in ./*.faa;
do
    sed -i "s/^>.*/&${file%%.*}/" "$file"
done

will append the file name at the end of the header (& in the replacement string evaluates to the string we are replacing, again effectively preserving it).

For another variation, try

for file in *.faa;
do
    sed -i "/^>/s/\$/ ${file%%.*}/" "$file"
done

which says on lines which match the regex ^>, replace the empty string at the end of the line $ with the file name.

Of course, your Awk script could easily be fixed, too. Standard Awk does not have an option to parallel the -i "in-place" option of sed, but you can easily use a temporary file:


for file in ./*.faa;
do
    awk '/>/{ $0 = $0 " " FILENAME);sub(/\.faa/,"")}1' "$file" >"$file.tmp" &&
    mv "$file.tmp" "$file"
done

GNU Awk also has an -i inplace extension which you could simply add to the options of your existing script if you have GNU Awk.

Since FASTA files typically contain multiple headers, adding to the header rather than replacing all headers in a file with the same string seems more useful, so I changed your Awk script to do that instead.

For what it's worth, the name of the character ^ is caret (carrot is