examples/sqlite/demo.sh fails with current pplacer. #6
Description
Could someone with some guppy DB experience lend a hand here (@nhoffman, @metasoarous)?
# `guppy classify` can build SQLite databases for easy and fast access to
# results.
guppy classify --mrca-class --sqlite example.db -c $SRC/vaginal_16s.refpkg $SRC/*.jplace
# Now we can investigate placement classifications using SQL queries. Here we
# ask for the lineage of a specific sequence.
sqlite3 -header example.db "
SELECT pc.rank,
tax_name,
likelihood
FROM placement_names AS pn
JOIN placement_classifications AS pc USING (placement_id)
JOIN taxa USING (tax_id)
JOIN ranks USING (rank)
WHERE pc.rank = desired_rank
AND pn.name = 'FUM0LCO01DX37Q'
ORDER BY rank_order
"
Error: no such column: pc.rankIs pc.rank deprecated?
FYI, it seems to me that the sanest way to run these tests is to run run_all.py and keep on hitting "n" until you get to this test.