obisilva fails with --ssu option
Obisilva fails when trying to download silva data with the --ssu option (with --ref or --parc option).
(OBITools-1.2.10) obisilva --ssu --ref
Traceback (most recent call last):
File "/usr/local/genome2/OBITools-1.2.10/export/bin/obisilva", line 319, in <module>
sequrl,taxurl,options.ecopcroutput = silvaURLS(options)
File "/usr/local/genome2/OBITools-1.2.10/export/bin/obisilva", line 190, in silvaURLS
taxurl = taxonomy[taxfile]
KeyError: 'tax_slv_ssu_nr_128.txt.gz'It seems that no file tax_slv_ssu_nr_128.txt, tax_slv_ssu_nr_128.txt.gz or tax_slv_ssu_nr_128.gz exist in http://ftp.arb-silva.de/release_128/Exports/taxonomy/
Obisilva works with the --lsu option.
Edit:
As Obisilva try to get a tax_slv_ssu_nr_128.txt file whitout --nr option, the problem seems to lie there.
Editing Obisilva with the attached patch seems to solve the issue.