Use d__ instead of sk__ in for contigs taxa (krona)

mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py

@@ -20,7 +20,7 @@
 from collections import Counter
 
 RANK_PREFIXES = {
-    "domain": "sk__",
+    "domain": "d__",
     "kingdom": "k__",
     "phylum": "p__",
     "class": "c__",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mgnify_pipelines_toolkit"
-version = "1.4.13"
+version = "1.4.14"
 readme = "README.md"
 license = { text = "Apache Software License 2.0" }
 authors = [

tests/fixtures/cat_classification/expected_output/krona.tsv

@@ -1,14 +1,14 @@
 9	unclassified
-5	sk__Bacteria	k__Bacillati	p__Bacillota
-3	sk__Bacteria	k__	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Rikenellaceae	g__Alistipes
-3	sk__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Oscillospiraceae
-1	sk__Eukaryota
-1	sk__Bacteria	k__Bacillati	p__Bacillota	c__	o__	f__	g__	s__Firmicutes bacterium CAG:822
-1	sk__Bacteria	k__Bacillati	p__Bacillota	c__	o__	f__	g__Candidatus Faecenecus	s__Candidatus Faecenecus gallistercoris
-1	sk__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Clostridiaceae	g__Clostridium	s__Clostridium sp. CAG:245_30_32
-1	sk__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Clostridiaceae	g__Clostridium	s__Clostridium sp. 27_14
-1	sk__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Clostridiaceae	g__Clostridium	s__Clostridium sp. 26_22
-1	sk__Bacteria	k__	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Bacteroidaceae	g__Phocaeicola	s__Phocaeicola dorei
-1	sk__Bacteria	k__	p__Pseudomonadota	c__Deltaproteobacteria	o__Desulfovibrionales	f__Desulfovibrionaceae	g__Desulfovibrio	s__Desulfovibrio piger
-1	sk__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__	g__Evtepia	s__Evtepia sp.
-1	sk__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Lachnospiraceae	g__Roseburia
+5	d__Bacteria	k__Bacillati	p__Bacillota
+3	d__Bacteria	k__	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Rikenellaceae	g__Alistipes
+3	d__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Oscillospiraceae
+1	d__Eukaryota
+1	d__Bacteria	k__Bacillati	p__Bacillota	c__	o__	f__	g__	s__Firmicutes bacterium CAG:822
+1	d__Bacteria	k__Bacillati	p__Bacillota	c__	o__	f__	g__Candidatus Faecenecus	s__Candidatus Faecenecus gallistercoris
+1	d__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Clostridiaceae	g__Clostridium	s__Clostridium sp. CAG:245_30_32
+1	d__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Clostridiaceae	g__Clostridium	s__Clostridium sp. 27_14
+1	d__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Clostridiaceae	g__Clostridium	s__Clostridium sp. 26_22
+1	d__Bacteria	k__	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Bacteroidaceae	g__Phocaeicola	s__Phocaeicola dorei
+1	d__Bacteria	k__	p__Pseudomonadota	c__Deltaproteobacteria	o__Desulfovibrionales	f__Desulfovibrionaceae	g__Desulfovibrio	s__Desulfovibrio piger
+1	d__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__	g__Evtepia	s__Evtepia sp.
+1	d__Bacteria	k__Bacillati	p__Bacillota	c__Clostridia	o__Eubacteriales	f__Lachnospiraceae	g__Roseburia

tests/unit/analysis/assembly/krona_txt_from_CAT_classification/test_krona_txt_from_cat_classification.yml

@@ -11,4 +11,6 @@
   exit_code: 0
   files:
     - path: "test_krona.txt"
-      md5sum: a017d47b6a2132e405dd77723fea1421
+      contains:
+        - "5\td__Bacteria\tk__Bacillati\tp__Bacillota"
+      md5sum: e2f367ec2d8be40a2841999424ac9064