metatran_LBE/20200723_infernal_search.sh
4b587de7d062master

20200723_infernal_search.sh
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			export DATABASE=/media/bioinfoteam/SCRATCH_850GB/databases/rna_profiles
			export INPUT=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/sequences
			export OUTPUT=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/infernal_output

			cd $INPUT

			for filename in $(ls *'.fasta')

			do
			echo $filename

			fileID=`expr match "$filename" '$[0-9]C_L1_R[1-2]$'`

			# search 16S rRNA genes
			cmsearch $DATABASE/RF00177.cm \
			$INPUT/$filename > $OUTPUT/${fileID}_16S_infernal.txt

			# search 23S rRNA genes
			cmsearch $DATABASE/RF02541.cm \
			$INPUT/$filename > $OUTPUT/${fileID}_23S_infernal.txt

			# search 5S rRNA genes
			cmsearch $DATABASE/RF00001.cm \
			$INPUT/$filename > $OUTPUT/${fileID}_5S_infernal.txt

			done