Fix incompatibility with gtfparse>=2 (#66)

icbi-lab · Jan 9, 2023 · 031d2c6 · 031d2c6
1 parent 74d28d9
commit 031d2c6
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -26,7 +26,7 @@ dependencies = [
     'numpy>=1.20', # includes type annotations
     'tqdm>=4.63.0', # fixes tqdm.auto
     'pytoml',
-    'gtfparse>=1.2.1',
+    'gtfparse>=2',
     'pycairo>=1.20; sys_platform == "win32"',
     'leidenalg',
     'pyreadr',

diff --git a/src/infercnvpy/io/_genepos.py b/src/infercnvpy/io/_genepos.py
@@ -38,7 +38,9 @@ def genomic_position_from_gtf(
     inplace
         If True, add the annotations directly to adata, otherwise return a dataframe.
     """
-    gtf = gtfparse.read_gtf(gtf_file, usecols=["seqname", "feature", "start", "end", "gene_id", "gene_name"])
+    gtf = gtfparse.read_gtf(
+        gtf_file, usecols=["seqname", "feature", "start", "end", "gene_id", "gene_name"], result_type="pandas"
+    )
     gtf = (
         gtf.loc[
             gtf["feature"] == "gene",