search

peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
8 stars 2 forks source link

Append classifier columns to sample-tally TSV #549

Closed peterjc closed 1 year ago

peterjc commented 1 year ago

With this the summary command won't need paired inputs. Will also want to update the assess command too...

Query: Do we want to preserve non-MD5 naming? Even if it masks duplicates?

peterjc commented 1 year ago

In addition to the summary command (done), and assess (pending), the old classifier TSV output is also used in edit-graph and curated-seq commands(for outputting a curated FASTA sequence).

Probably want to accept the tally-with-species TSV file instead of FASTA + (legacy) TSV?

peterjc commented 1 year ago

I'm leaning towards dropping the curated-seq command, perhaps in favour of simple entry under scripts/, as this would reduce the command line options clutter.

peterjc commented 1 year ago

OK, that's summary and edit-graph updated to work with the classifier output directly; curated-seq dropped.

Just the assess command still pending - the most tricky, cross reference #425. Currently still using XXX.tally.tsv plus XXX.method.tsv, or pairs of legacy per-sample TSV.