Skip to content

Add no_rank to ranks #61

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
audy merged 3 commits into from
Mar 17, 2025
Merged

Add no_rank to ranks #61

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
ea0c04b
Add `no_rank` to ranks
audy Mar 15, 2025
77dc217
Use dynamic version
audy Mar 15, 2025
11e73d0
Fix test
audy Mar 17, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ build-backend = "maturin"

[project]
name = "taxonomy"
dynamic = ["version"]
classifier = [
"Intended Audience :: Science/Research",
"Programming Language :: Python :: 3",
Expand Down
2 changes: 2 additions & 0 deletions src/formats/ncbi.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@
Ok(gt)
}

pub fn save<'t, T: 't, P: AsRef<Path>, X: Taxonomy<'t, T>>(

Check warning on line 86 in src/formats/ncbi.rs

View workflow job for this annotation

GitHub Actions / clippy 

bound is defined in more than one place
tax: &'t X,
out_dir: P,
) -> TaxonomyResult<()>
Expand Down Expand Up @@ -127,6 +127,7 @@
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|
Expand All @@ -137,6 +138,7 @@
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|
Expand Down
2 changes: 1 addition & 1 deletion src/rank.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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),
Expand Down
2 changes: 1 addition & 1 deletion test_python.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
1 change: 1 addition & 0 deletions tests/data/names.dmp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,3 +48,4 @@
91347 | Enterobacterales | | scientific name |
131567 | biota | | synonym |
131567 | cellular organisms | | scientific name |
10239 | Viruses | | scientific name |
1 change: 1 addition & 0 deletions tests/data/nodes.dmp
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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 | |
Expand Down
Loading