From ba1fd3e421b993abc6e73d8e38e4d52509afbfca Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 28 Sep 2023 07:23:54 -0700 Subject: [PATCH] MRG: update docs for tax grep: only searches tax (#2789) Updates `tax grep` documentation to make it clear that it only searches taxonomic ranks, not identifiers; `sig grep` searches sketch names. Fixes https://github.com/sourmash-bio/sourmash/issues/2607 --- doc/command-line.md | 3 +++ src/sourmash/cli/tax/grep.py | 5 ++++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/command-line.md b/doc/command-line.md index eda5b2ac2c..640ff9c9a5 100644 --- a/doc/command-line.md +++ b/doc/command-line.md @@ -1041,6 +1041,9 @@ superkingdom, phylum, class, order, family, genus, and species. to ignore case and `-v` to output only taxonomic lineages that do _not_ match the pattern. +Note: `tax grep` only searches taxonomic ranks, not identifier strings. +Use `sig grep` to search for identifiers in sketch collections. + Currently only CSV output (optionally gzipped) is supported; use `sourmash tax prepare` to convert CSV output from `tax grep` into a sqlite3 taxonomy database. diff --git a/src/sourmash/cli/tax/grep.py b/src/sourmash/cli/tax/grep.py index 003c152dc1..9aa5db3b89 100644 --- a/src/sourmash/cli/tax/grep.py +++ b/src/sourmash/cli/tax/grep.py @@ -1,4 +1,4 @@ -"""search taxonomies and output picklists..""" +"""search taxonomies and output picklists.""" usage=""" @@ -9,6 +9,9 @@ It creates new files containing matching taxonomic entries; these new files can serve as taxonomies and can also be used as picklists. +`tax grep` only searches taxonomic ranks, not identifier strings. +Use `sig grep` to search for identifiers in sketch collections. + Please see the 'tax grep' documentation for more details: https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-grep-subset-taxonomies-and-create-picklists-based-on-taxonomy-string-matches """