reformat: accept input of both (partly) lineage and taxids :) #42

CHANGELOG.md

@@ -1,6 +1,9 @@
-- [TaxonKit v0.7.3](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.3)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.7.3/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.3)
+- [TaxonKit v0.8.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.8.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.8.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.8.0)
     - `taxonkit reformat`:
+        - **accept input of TaxIds via flag `-I/--taxid-field`**.
+        - **accept single taxonomy names**.
+        - show warning message for TaxIds with the same lineage. [#42](https://github.com/shenwei356/taxonkit/issues/42)
         - better flag checking. [#40](https://github.com/shenwei356/taxonkit/issues/40)
     - `taxonkit lca`:
         - slightly speedup.

taxonkit/cmd/lineage.go

@@ -55,8 +55,9 @@ Output:
      - New TaxIds for merged TaxIds, provided by "merged.dmp".
      - Taxids for these found in "nodes.dmp".
   3. Lineage, delimiter can be changed with flag -d/--delimiter.
-  4. (Optional) Lineage in TaxIds (-t/--show-lineage-taxids)
-  5. (Optional) Rank (-r/--show-rank)
+  4. (Optional) TaxIds taxons in the lineage (-t/--show-lineage-taxids)
+  5. (Optional) Name (-n/--show-name)
+  6. (Optional) Rank (-r/--show-rank)
 
 Filter out invalid and deleted taxids, and replace merged 
 taxids with new ones: