There is a new sRNAtoolbox version! You can find it here
sRNAbench can read specially prepared annotations, i.e. the transcript name and the classification separated by ‘:’. The 'Ensembl Parser' reads a Ensembl fasta annotation file and generates the sRNAbench format. In can use cDNA and ncRNA fasta files from this page .
If you use this data please cite: Paul Flicek et al. (2012). Ensembl 2013. Nucleic Acids Res.