There is a new sRNAtoolbox version! You can find it here

NCBI Parser:

sRNAbench can read specially prepared annotations, i.e. the transcript name and the classification separated by ‘:’. The 'NCBI Parser' reads a NCBI fasta annotation file and generates the sRNAbench format. In can use *.rna.fna.gz files from the following page .

Link to test data

If you use this data please cite: Kim D. Pruitt et al. (2012). NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. PMCID: PMC3245008.