I'm running the bioinformatics tool hmmer and I would like to run it for over 7000 test sequence queries. After it runs each one, I would like it to save the output in a text file, which it does quite easily.
I am trying to create a for loop in bash that would run hmmer on each test sequence in the folder and writes the output to its own text file.
How does one write a statement inside the for loop so that it writes to a different text file each time the loop is performed?
Currently my code is as such
for i in First10/*; do binaries/jackhmmer --tblout test[i].txt -E1 --noali $i largedatabase.fasta done