Extract 16S rRNA from genomes

If you find this script useful please cite:
Campanaro S, Treu L, Kougias PG, Luo G, Angelidaki I. Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants. Water Res. 2018 Sep 1;140:123-134. doi:10.1016/j.watres.2018.04.043.

This script extracts 16S rRNA sequences from multifasta files present in the folder reported as first argument.
It works only in unix system and requires nhmmer and samtools software installed in the system path (if not in system path modify the path at lines 21,72 (for nhmmer),51,100 (for samtools) of the script by adding the path to your nhmmer executable).
The HMM files arc.ssu.rnammer.hmm and bac.ssu.rnammer.hmm have to be in the same software were executable file is saved.
Inside the folder creates two sub-folders named "bacteria" and "archaea" where you will save your multifasta files (multifasta of bacteria in one and of archaea in the other one).
MORE DETAILS IN THE FILE INCLUDED...