I'm currently working on a script to modify header information in a FASTA file that contains thousands of protein accessions. I have a taxonomy information file that provides the necessary lineage data. My goal is to read through each header, extract the accession number and species name, retrieve the corresponding taxonomy information, and update the header with this taxonomy info using 'sed'. However, the script runs extremely slowly due to the multiple external commands. Here's a snippet of what I'm working with:
```bash
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/" "$dir_partial/blast-results_5000_formatted.fasta"
done < " "$blastout")
```
For context, an original FASTA 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 make this process faster?
1 Answer
Using bash's built-in features instead of external commands can really speed things up. Consider changing your logic to reduce the number of subshells. For instance, instead of calling `cut` and `sed` for every line, you could directly handle the string manipulations in bash. For example, you can use parameter expansions and regex matching to extract the accession and species without needing external commands. Here's a simplified version of what you could do:
```bash
while read -r line
do
accession="${line%% *}"
species="${line#*[}"
species="${species%%]*}"
# Lookup and processing logic here...
done < " "$blastout")
```
Also, pulling in your taxonomy data into an associative array once at the beginning can save time. This way, you don’t keep searching through the same file repeatedly.
Also consider looking into using `awk` as it can be very efficient for text processing and could replace a lot of your `sed` and `grep` calls.
You might also want to try out `xargs` or GNU `parallel` to utilize multiple cores if your machine has them. It can significantly speed up your processing time.