quick update

Author: y9c

metagene/annotation.py

@@ -25,7 +25,7 @@ def map_to_transcripts(
     exon_pr = pr.PyRanges(exon_ref.to_pandas())  # type: ignore
 
     # Perform join operation
-    annot_pr = exon_pr.join_ranges(  # type: ignore
+    annot_pr = exon_pr.join_overlaps(  # type: ignore
         input_pr,
         suffix="_qry",
         join_type="inner",

metagene/gtf.py

@@ -167,7 +167,7 @@ def prepare_exon_ref(gtf_file: str) -> pl.DataFrame:
     pr_codons = pr.PyRanges(pl_df_codons.to_pandas())
     # Join with exon reference and calculate positions
     df_codons = (
-        pr_exon.join_ranges(pr_codons, join_type="inner", match_by="transcript_id")  # type: ignore
+        pr_exon.join_overlaps(pr_codons, join_type="inner", match_by="transcript_id")  # type: ignore
         .assign(
             codon_pos=lambda df: np.where(
                 df["Strand"] == "+",

metagene/overlap.py

@@ -92,10 +92,10 @@ def annotate_with_features(
     Returns:
         Tuple of (annotated dataframe, binned statistics)
     """
-    # Perform overlap using PyRanges v1 join_ranges
+    # Perform overlap using PyRanges v1 join_overlaps
     df_joined = (
         pr.PyRanges(df_input)
-        .join_ranges(
+        .join_overlaps(
             pr.PyRanges(df_feature),
             report_overlap_column="Overlap",
             strand_behavior="same" if by_strand else "ignore",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "metagene"
-version = "0.0.13"
+version = "0.0.14"
 description = "Metagene Profiling Analysis and Visualization"
 authors = [{ name = "Ye Chang", email = "yech1990@gmail.com" }]
 requires-python = ">=3.12"

scripts/process_gtf_to_parquet.py

@@ -178,7 +178,7 @@ def prepare_exon_ref(gtf_file: str) -> pr.PyRanges:
     pr_codons = pr.PyRanges(pl_df_codons.to_pandas())
     # Join with exon reference and calculate positions
     df_codons = (
-        pr_exon.join_ranges(pr_codons, join_type="inner", match_by="transcript_id")
+        pr_exon.join_overlaps(pr_codons, join_type="inner", match_by="transcript_id")
         .assign(
             codon_pos=lambda df: np.where(
                 df["Strand"] == "+",