examples/sqlite/demo.sh fails with current pplacer.

[matsen]

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.rank

Is 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.

[metasoarous]

I can check that out.

On Tue, Feb 11, 2014 at 5:54 AM, Erick Matsen [email protected]:

Could someone with some guppy DB experience lend a hand here (@nhoffmanhttps://github.com/nhoffman,
@metasoarous https://github.com/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, likelihoodFROM 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.rank

Is 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.

Reply to this email directly or view it on GitHubhttps://github.com//issues/6
.

Christopher Small
Systems Analyst Programmer - Matsen Group
Fred Hutchinson Cancer Research Center
[email protected]