wheretrue/biobear

Deprecation points to non-existent docs

jguhlin opened this issue · 4 comments

jguhlin commented 
DeprecationWarning: FastaReader is being deprecated, please use a table function via the session.
See https://www.wheretrue.dev/docs/exon/exondb/api-reference/table-functions for more info.

That link leads to a "Page Not Found" error

Generated from this code:

bb.FastaReader(seqfile).to_arrow()

(So not using exon)

tshauck commented

Sorry about that... will update to https://www.wheretrue.dev/docs/exon/sql-reference#table-functions.

For FastaReader it'd be:

session = bb.connect()
seqfile = 'test.fasta'

arrow = session.sql(f"""
SELECT *
FROM fasta_scan('{seqfile}')
""").to_arrow()

FWIW I'm not totally sold on deprecating, so please let me know what you think.

jguhlin commented
tshauck commented

Cool, yeah, I got a bit of a wild hair, but agree and'll probably leave them in.

jguhlin commented