Identification of motifs fails with lower-case fasta reference sequences

[tfwulff]

Thanks for your great tool!

I encountered a problem when using a reference genome fasta file with lower-case alphabet: Although motifs were identified by STREME, no motifs were listed in the final LIBRARY_NAME_motifs.tsv output file. It turned out that STREME transforms input sequences to upper-case letters by default, which makes microbemod.py fail when trying to find motif occurrences in the lower-case reference sequence (lines 335 to 347).
May be worth to mention this behaviour in the parameter description, took me some time to figure out what the problem was.

[alexcritschristoph]

Thanks for catching this case! Will try to update to fix it soon.