fix multiqc folder creation part 2

TRISTAN-ORF · Dec 2, 2024 · 4dc3e26 · 4dc3e26
1 parent 720cacd
commit 4dc3e26
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/transcript_transformer/processing.py b/transcript_transformer/processing.py
@@ -756,7 +756,7 @@ def create_multiqc_reports(df, out_prefix):
         orf_biotypes = (
             df.filter(pl.col("ORF_type") == "varRNA-ORF")["transcript_biotype"]
             .value_counts()
-            .sort(pl.col("transcript_biotype").cast(pl.Enum(ORF_BIOTYPE_ORDER)))
+            .sort("count", descending=True)
         )
         with open(output, mode="a") as f:
             orf_biotypes.write_csv(f, separator="\t", include_header=False)

diff --git a/transcript_transformer/ribotie.py b/transcript_transformer/ribotie.py
@@ -229,9 +229,15 @@ def main():
             )
             if df is not None:
                 csv_to_gtf(args.h5_path, df, out_prefix, args.exclude_annotated)
-                os.makedirs(f"{os.path.dirname(args.out_prefix)}/multiqc", exist_ok=True)
+                os.makedirs(
+                    os.path.join(os.path.dirname(args.out_prefix), "multiqc"),
+                    exist_ok=True,
+                )
                 create_multiqc_reports(
-                    df, f"{os.path.dirname(args.out_prefix)}/multiqc/{ribo_set_str}"
+                    df,
+                    os.path.join(
+                        os.path.dirname(args.out_prefix), "multiqc", ribo_set_str
+                    ),
                 )