I'm dealing with a FASTA file that has thousands of protein accessions and I want to replace the header information with taxonomy details. I have a file containing taxonomy data and I'm using a loop to read through each header line, extract the accession number and species, find the taxonomy lineage corresponding to the species, and then substitute the header with this new information using `sed`. However, the code is running really slow. Here's the approach I'm using:
while read -r line
do
accession="$(echo "$line" | cut -f 1 -d " " | sed 's/>//')"
species="$(echo "$line" | cut -f 2 -d "[" | sed 's/]//')"
taxonomy="$(grep "$species" "$dir_partial/lineages.txt" | head -n 1)"
kingdom="$(echo "$taxonomy" | cut -f 2)"
order="$(echo "$taxonomy" | cut -f 4)"
newname="$(echo "${kingdom}-${order}_${species}_${accession}" | tr " " "-")"
sed -i "s/>$accession.*/>$newname/" "$dir_partial/blast-results_5000_formatted.fasta"
done < <(grep ">" "$blastout")
For example, the original header looks like this:
>XP_055356955.1 uncharacterized protein LOC129602037 isoform X2 [Paramacrobiotus metropolitanus] and I want to change it to something like >Metazoa-Eutardigrada_Paramacrobiotus-metropolitanus_XP_055356955.1. Any tips to speed this up?
4 Answers
Using commands like `cut`, `grep`, and `sed` for each header is really slowing you down because they create subshells, which are expensive in a loop. You should minimize these calls. Try using bash's built-in string manipulation features instead.
Here's an optimized version:
while read -r accession other; do
accession="${accession#>}"
[[ $other =~ [(.*)]$ ]] && species="${BASH_REMATCH[1]}"
taxonomy="$(awk -F 't' -v species="$species" '$3 ~ species { print $2, $4; exit; }' "$dir_partial/lineages.txt")"
newname="${taxonomy// /-}_${species}_${accession}"
sed -i "s/>$accession.*/>$newname/" "$dir_partial/blast-results_5000_formatted.fasta"
done < <(grep ">" "$blastout")
This will significantly reduce the number of subshell invocations and should speed things up a lot!
Also consider using `parallel` or `xargs` to take advantage of multiple cores on your machine. It could substantially reduce processing time.
Honestly, if you're hitting performance issues, it might be worth looking into switching to a more appropriate programming language like Python or Perl for this task. They handle string manipulation and file operations much more efficiently for tasks like these. You'll find them easier to work with as well, especially as your code gets more complex.
The idea of moving to a different toolset altogether may also be beneficial! While bash is powerful, sometimes languages like `awk` or `R` might be much faster for this specific job. They can process files more efficiently in one go instead of line by line.
You're really triggering performance limits with your current bash approach. Each time you call an external command, you're opening a subshell and that adds overhead.
You could read your `lineages.txt` file once and build a mapping in an associative array (if you have bash 4.0 or newer). This way, you can lookup taxonomy data without repeatedly scanning the file. Here’s a quick example:
declare -A taxonomyMap
while read -r _ king _ order spc; do
taxonomyMap[$spc]="$king-$order"
done < "${dir_partial}/lineages.txt"
while read -r line; do
# parse line and do replacements using taxonomyMap
done < " "$blastout")
This should provide you with a significant speedup!
Great tips! Just be cautious with `sed` as it can still be slow. Maybe try loading your FASTA file into memory and manipulating it there before writing it back.