Merge pull request #61 from onecodex/audy/add-no-rank-rank

Add `no_rank` to ranks

Author: audy

pyproject.toml

@@ -4,6 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "taxonomy"
+dynamic = ["version"]
 classifier = [
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3",

src/formats/ncbi.rs

@@ -127,6 +127,7 @@ mod tests {
     fn can_import_ncbi() {
         let nodes =
             "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|
+    10239\t|\t1\t|\tno_rank\t|\t\t|\t9\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|
     2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|
     543\t|\t91347\t|\tfamily\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|
     561\t|\t543\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|
@@ -137,6 +138,7 @@ mod tests {
     131567\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|";
         let names = "1\t|\tall\t|\t\t|\tsynonym\t|
     1\t|\troot\t|\t\t|\tscientific name\t|
+    10239\t|\tViruses\t|\t\t|\tscientific name\t|
     2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|
     543\t|\tEnterobacteriaceae\t|\t\t|\tscientific name\t|
     561\t|\tEscherchia\t|\t\t|\tmisspelling\t|

src/rank.rs

@@ -239,7 +239,7 @@ impl FromStr for TaxRank {
             "breed" => Ok(TaxRank::Breed),
             "strain" => Ok(TaxRank::Strain),
             "serogroup" => Ok(TaxRank::SeroGroup),
-            "no rank" => Ok(TaxRank::Unspecified),
+            "no rank" | "no_rank" => Ok(TaxRank::Unspecified),
             "biotype" => Ok(TaxRank::Biotype),
             "clade" => Ok(TaxRank::Clade),
             "forma specialis" => Ok(TaxRank::FormaSpecialis),

test_python.py

@@ -394,7 +394,7 @@ def test_prune(self):
         new_tax = self.tax.prune(remove=["561"])
         self.assertIsNone(new_tax.node("561"))
         self.assertIsNone(new_tax.node("562"))
-        self.assertEqual(len(new_tax), 7)
+        self.assertEqual(len(new_tax), 8)
 
         new_tax = self.tax.prune(keep=["561"])
         self.assertEqual(len(new_tax), 8)

tests/data/names.dmp

@@ -48,3 +48,4 @@
 91347	|	Enterobacterales	|		|	scientific name	|
 131567	|	biota	|		|	synonym	|
 131567	|	cellular organisms	|		|	scientific name	|
+10239	|	Viruses	|		|	scientific name	|

tests/data/nodes.dmp

@@ -1,4 +1,5 @@
 1	|	1	|	no rank	|		|	8	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
+10239	|	1	|	no_rank	|		|	9	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
 2	|	131567	|	superkingdom	|		|	0	|	0	|	11	|	0	|	0	|	0	|	0	|	0	|		|
 543	|	91347	|	family	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
 561	|	543	|	genus	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|