fix compress output in proksee and suffix mamangement in write_compre…

…ssed_or_not fct
labgem · Nov 23, 2023 · 8ebbf4a · 8ebbf4a
1 parent 1be04d6
commit 8ebbf4a
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diff --git a/ppanggolin/formats/writeFlatGenomes.py b/ppanggolin/formats/writeFlatGenomes.py
@@ -442,7 +442,7 @@ def mp_write_genomes_file(organism: Organism, output: Path, organisms_file: Path
 
         # Write ProkSee data for the organism
         write_proksee_organism(organism, output_file, features=['all'], genome_sequences=genome_sequences,
-                               **{arg: kwargs[arg] for arg in kwargs.keys() & {'module_to_colors'}})
+                               **{arg: kwargs[arg] for arg in kwargs.keys() & {'module_to_colors', 'compress'}})
 
     if gff:
         gff_outdir = output / "gff"

diff --git a/ppanggolin/utils.py b/ppanggolin/utils.py
@@ -225,7 +225,7 @@ def write_compressed_or_not(file_path: Path, compress: bool = False) -> Union[gz
     :return: file-like object, compressed or not
     """
     if compress:
-        return gzip.open(file_path.with_suffix(".gz"), mode="wt")
+        return gzip.open(file_path.parent / (file_path.name + '.gz'), mode="wt")
     else:
         return open(file_path, "w")