Including file name of database into blast output

Question

[tariela]

Hi everyone, can you please advise me on how to include the file name of my database into the output of blast while using outfmt 6?

The example below - I need the ${file} included in every ${file}.blast output file, so I could merge all the ${file}.blast files into one and still know which database ${file} did the sequence come from.

makeblastdb -in ${file}.fa -dbtype nucl -out ${file}

blastn -query query.fasta -db ${file} -out ${file}.blast -outfmt "6 qseqid sseqid pident length qstart qend sstart send evalue bitscore sseq" -num_threads 36 -max_target_seqs 5 -task blastn

Perhaps I am missing some obvious way. I'd prefer not to rename all the sequences in the database files and I'd rather not use outfmt 7 where I could get the database file name in the comment.

Thank you all so much, this is my first post.

Answer 1

[Istvan Albert]

As far as I know, the database name is not available as an outfmt template parameter.

As a workaround you could prepend that information in your script:

echo "# dbname=${file}.fa > results.txt
blastn .... >> results.txt

interestingly there are other pieces of information that are only available with outfmt 7, not getting a hit with a query is mentioned in the comments of format 7 but not in format 6