v0.2.0

xinehc · Jan 12, 2025 · c783982 · c783982
1 parent 426f9aa
commit c783982
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,11 @@
 # Changelog
+## [0.2.0] - 2025-01-12
+### Changed
+- [***breaking***] Simplify command line interface (`-I` -> `-i`, `-S` -> `-s`), options related genome copy estimation are removed.
+### Added
+- Add `--skip-melon` for skipping genome copy estimation.
+
+
 ## [0.1.3] - 2024-11-15
 ### Changed
 - Change default mode (without `--plasmid`) to classifying all reads that carry ARGs.

diff --git a/README.md b/README.md
@@ -59,9 +59,9 @@ INFO: ... found 8 unique species (bacteria: 8; archaea: 0).
 INFO: Overlapping ...
 INFO: ... median sequence divergence: 0.0519 | initial identity cutoff: 0.9 * 77.03.
 INFO: Annotating ARGs ...
-INFO: ... candidate HSPs: 11316 | ARG-containing reads: 632.
+INFO: ... candidate HSPs: 11315 | ARG-containing reads: 632.
 INFO: Overlapping of ARG-containing reads ...
-INFO: ... median sequence divergence of ARG-containing reads: 0.0503 | identity cutoff: 77.41 | low-identity HSPs: 3621.
+INFO: ... median sequence divergence of ARG-containing reads: 0.0503 | identity cutoff: 77.41 | low-identity HSPs: 3620.
 INFO: Assigning taxonomy ...
 INFO: Graph clustering ...
 INFO: ... read clusters: 169 | low-subject-cover HSPs: 524 | overlapping HSPs: 6336 | remaining HSPs: 835
@@ -92,17 +92,17 @@ Output file `example.sarg.json` contains detailed annotation information for ARG
         "hit": [
             "multidrug@MFS|norA|WP_001041272.1"
         ],
-        "lineage": "Bacteria;Bacillota;Bacilli;Staphylococcales;Staphylococcaceae;Staphylococcus;Staphylococcus aureus",
-        "plasmid": false
+        "plasmid": false,
+        "lineage": "Bacteria;Bacillota;Bacilli;Staphylococcales;Staphylococcaceae;Staphylococcus;Staphylococcus aureus"
     },
     ...
     "b62a8716-65cb-4170-9a8c-3c7f87e78fea": {
         "remark": "ARG-containing",
         "hit": [
             "tetracycline|tet(L)|WP_001574277.1"
         ],
-        "lineage": "Bacteria;Bacillota;Bacilli;Staphylococcales;Staphylococcaceae;Staphylococcus;Staphylococcus aureus",
-        "plasmid": true
+        "plasmid": true,
+        "lineage": "Bacteria;Bacillota;Bacilli;Staphylococcales;Staphylococcaceae;Staphylococcus;Staphylococcus aureus"
     },
     ...
 }

diff --git a/src/argo/__init__.py b/src/argo/__init__.py
@@ -1,3 +1,3 @@
-__version__ = '0.1.3'
+__version__ = '0.2.0'
 
 from .argo import AntibioticResistanceGeneProfiler