From 199f3a50f183dc3acd3d0d55fa0d339e0becf91e Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 6 Dec 2024 16:16:02 -0800
Subject: [PATCH] Improve typing in fasta_to_csv

---
 micall/tests/test_fasta_to_csv.py | 4 ++--
 micall/utils/contig_summary.py    | 2 +-
 micall/utils/fasta_to_csv.py      | 8 ++++----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/micall/tests/test_fasta_to_csv.py b/micall/tests/test_fasta_to_csv.py
index 4ab951b6d..0fe8a92c1 100644
--- a/micall/tests/test_fasta_to_csv.py
+++ b/micall/tests/test_fasta_to_csv.py
@@ -16,7 +16,7 @@ def DEFAULT_DATABASE():
 
 @pytest.fixture(scope='session', name='hcv_db')
 def check_hcv_db(DEFAULT_DATABASE):
-    db_path = Path(DEFAULT_DATABASE)
+    db_path = DEFAULT_DATABASE
     index_path = db_path.parent / "refs.fasta.nin"
     build_needed = not index_path.exists()
     if not build_needed:
@@ -32,7 +32,7 @@ def check_hcv_db(DEFAULT_DATABASE):
 
 
 def test_make_blast_db_excludes_hivgha(hcv_db, DEFAULT_DATABASE):
-    fasta_path = Path(DEFAULT_DATABASE)
+    fasta_path = DEFAULT_DATABASE
     with fasta_path.open() as f:
         for reference in SeqIO.parse(f, 'fasta'):
             # Exclude the Ghana project, because they're recombinant.
diff --git a/micall/utils/contig_summary.py b/micall/utils/contig_summary.py
index e4ba399d2..7b8529b99 100644
--- a/micall/utils/contig_summary.py
+++ b/micall/utils/contig_summary.py
@@ -52,7 +52,7 @@ def main():
             with default_database() as DEFAULT_DATABASE:
                 stdout = Blastn().genotype(
                     contigs_fasta=contigs_fasta_path,
-                    database=Path(DEFAULT_DATABASE),
+                    database=DEFAULT_DATABASE,
                 )
             plot_contigs(sample_dir, stdout)
             plot_path = contig_plots_path / (sample_dir.name + '.png')
diff --git a/micall/utils/fasta_to_csv.py b/micall/utils/fasta_to_csv.py
index cd7616e19..fcd762ea6 100644
--- a/micall/utils/fasta_to_csv.py
+++ b/micall/utils/fasta_to_csv.py
@@ -55,9 +55,9 @@ def reference_dir() -> Iterator[Path]:
 
 
 @contextlib.contextmanager
-def default_database() -> Iterator[str]:
+def default_database() -> Iterator[Path]:
     with reference_dir() as blast_db:
-        yield str(blast_db / "refs.fasta")
+        yield blast_db / "refs.fasta"
 
 
 def read_assembled_contigs(group_refs: Dict[str, str],
@@ -134,7 +134,7 @@ def write_contigs(writer: DictWriter,
                              contig=contig.seq))
 
 
-def genotype(fasta: str, db: Optional[str] = None,
+def genotype(fasta: str, db: Optional[Path] = None,
              blast_csv: Optional[TextIO] = None,
              group_refs: Optional[Dict[str, str]] = None) -> Dict[str, typing.Tuple[str, float]]:
     """Use Blastn to search for the genotype of a set of reference sequences.
@@ -166,7 +166,7 @@ def genotype(fasta: str, db: Optional[str] = None,
                      'sstart',
                      'send']
 
-    def invoke_blast(db: str) -> str:
+    def invoke_blast(db: Path) -> str:
         return Blastn().genotype(
             contigs_fasta=Path(fasta),
             database=Path(db),