Merge pull request #28 from geneontology/fix_goref

updating makefile commands
geneontology · Feb 13, 2024 · 7018e9e · 7018e9e
2 parents c555506 + 7bc611a
commit 7018e9e
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/Makefile b/Makefile
@@ -41,7 +41,7 @@ convert_human:
 	poetry run convert_annotations --namespaces 'HUMAN','UniProtKB' --target_taxon "NCBITaxon:10090" --source_taxon "NCBITaxon:9606" --ortho_reference "GO_REF:0000119"
 
 convert_rat:
-	poetry run convert_annotations
+	poetry run convert_annotations --ortho_reference "GO_REF:0000096" --target_taxon "NCBITaxon:10090" --source_taxon "NCBITaxon:10116" --namespaces 'RGD'
 
 compare_human:
 	poetry run compare -file1 Lori_human.tsv -file2 mgi-human-ortho.gaf -o compare_human

diff --git a/src/gopreprocess/cli.py b/src/gopreprocess/cli.py
@@ -39,7 +39,7 @@ def cli():
     help="Source taxon in curie format using NCBITaxon prefix, e.g. NCBITaxon:10116",
 )
 @click.option(
-    "--ortho_reference", default="GO_REF:0000096", help="Ortho reference in curie format, e.g. GO_REF:0000096"
+    "--ortho_reference", help="Ortho reference in curie format, e.g. GO_REF:0000096"
 )
 def convert_annotations(namespaces, target_taxon, source_taxon, ortho_reference):
     """Converts annotations from one taxon to another using orthology."""