The pipeline was saving the alignment character string for each putative hit, since it's returned by BLAST anyway. However, it would probably be better to have the full query sequence, since the alignment sequence that BLAST outputs is often shorter than the query sequence and contains gap characters.
Rather than adding another column to the pipeline output csv, this just replaces the alignment sequence with the ORF amino acid sequence in the output.
The pipeline was saving the alignment character string for each putative hit, since it's returned by BLAST anyway. However, it would probably be better to have the full query sequence, since the alignment sequence that BLAST outputs is often shorter than the query sequence and contains gap characters.
Rather than adding another column to the pipeline output csv, this just replaces the alignment sequence with the ORF amino acid sequence in the output.