There was a problem where the utilities.determine_species(...) function was expecting a filename, but was being passed a read object instead, so Refseq Masher was always failing and the species was being reported as "Unknown".
The related tests were passing because the tests were passing the filename correctly.
Also, changed the way additional major species are output:
for species in species_list[1:min(5, len(species_list))]:
click.echo(species)
This is because now that species are being output correctly, there's A LOT of them being estimated at low probability. The above change will limit how many are printed to output, but will not otherwise change the behaviour of assemble.
There was a problem where the utilities.determine_species(...) function was expecting a filename, but was being passed a read object instead, so Refseq Masher was always failing and the species was being reported as "Unknown".
The related tests were passing because the tests were passing the filename correctly.
Also, changed the way additional major species are output:
This is because now that species are being output correctly, there's A LOT of them being estimated at low probability. The above change will limit how many are printed to output, but will not otherwise change the behaviour of assemble.