Exposing --species-like for amr queries #33

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1. thanhleviet

   closed this as completedin #41on Aug 5, 2026
2. thanhleviet commented on Aug 5, 2026

   

   thanhleviet

   on Aug 5, 2026

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   Implemented in #41, now on main.

   atb amr accepts --species-like, so your command works as written:

   atb amr --hq-only --species-like "Campylobacter_D jej%" --format tsv --output $ORG_DIR/raw_${ORG_DIR}_AMRFP.tsv

   Pattern rule. % matches any sequence of characters; every other character, including _, matches itself. GTDB clade names such as Campylobacter_D and Enterococcus_B therefore work as typed. atb query --species-like follows the same rule.

   It is not a full scan. The AMR data is partitioned per genus, and the literal text before the first % decides which partition files can hold a match. "Campylobacter_D jej%" reads only the Campylobacter_D partition (plus the shared partition that holds genera too small for their own file, which is ~2% of samples). "Streptococcus%" reads every Streptococcus* partition. Only a pattern that starts with % names no genus and has to scan the full dataset, and in that case the command prints a note telling you so and suggesting you anchor the pattern.

   --species-like also counts as a filter for the "scan everything?" confirmation, so it does not ask for --yes.

   Verified against the real dataset with exactly the command above: 277,638 rows, covering Campylobacter_D jejuni, Campylobacter_D jejuni_A, and Campylobacter_D jejuni_D. That last detail is worth flagging - the two lettered sub-clades are ones an exact --species "Campylobacter_D jejuni" match drops silently, so the wildcard is likely giving you a more complete answer than the exact flag would have.

   One related fix rode along: patterns with an interior wildcard, such as "Enterococcus%faecium" (the form the docs recommend for searching across GTDB naming variants), previously fell back to an exact string comparison on one of the two execution paths. Both paths now share a single matcher, so they agree.

   A release including this is being cut now; I will follow up here with the version.
3. thanhleviet commented on Aug 5, 2026

   

   thanhleviet

   on Aug 5, 2026

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   Released in v0.19.0 - atb amr --species-like "Campylobacter_D jej%" now works, reading only the matching genus partitions rather than scanning the full dataset.

   Upgrade with the installer or grab a binary from the release page; releases/latest now points at v0.19.0.