get_converter receives args. get_lifter receives source and dest asse…

…mblies.
rkimoakbioinformatics · Dec 8, 2023 · f20cda6 · f20cda6
1 parent 9b13197
commit f20cda6
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/oakvar/__init__.py b/oakvar/__init__.py
@@ -135,13 +135,13 @@ def get_mapper(module_name, input_file=None):
     return module
 
 
-def get_converter(module_name):
+def get_converter(module_name, *args, **kwargs):
     module = None
     ModuleClass = get_module(module_name, module_type="converter")
     if ModuleClass:
         module = ModuleClass()
         module.name = module_name
-        module.setup()
+        module.setup(*args, **kwargs)
     return module
 
 

diff --git a/oakvar/lib/base/master_converter.py b/oakvar/lib/base/master_converter.py
@@ -490,7 +490,7 @@ def collect_input_file_handles(self):
             encoding = self.get_file_object_for_input_path(input_path)
             self.input_file_handles[input_path] = encoding
 
-    def setup(self):
+    def setup(self, *args, **kwargs):
         self.collect_converter_paths()
         self.collect_input_file_handles()
         self.collect_converter_name_by_input()

diff --git a/oakvar/lib/util/seq.py b/oakvar/lib/util/seq.py
@@ -382,7 +382,7 @@ def reverse_complement(bases):
     return "".join([complementary_base[base] for base in bases[::-1]])
 
 
-def get_lifter(source_assembly: str) -> Optional[ChainFile]:
+def get_lifter(source_assembly: str, to_assembly: str="") -> Optional[ChainFile]:
     """get_lifter.
 
     Args:
@@ -401,7 +401,9 @@ def get_lifter(source_assembly: str) -> Optional[ChainFile]:
         return None
     if not liftover_dir.exists():
         makedirs(liftover_dir, exist_ok=True)
-    chain_file_basename = f"{source_assembly.lower()}To{SYSTEM_GENOME_ASSEMBLY.capitalize()}.over.chain.gz"
+    if not to_assembly:
+        to_assembly = SYSTEM_GENOME_ASSEMBLY
+    chain_file_basename = f"{source_assembly.lower()}To{to_assembly.capitalize()}.over.chain.gz"
     chain_file_path: Path = liftover_dir / chain_file_basename
     if not chain_file_path.exists():
         url = f"https://hgdownload.cse.ucsc.edu/goldenPath/{source_assembly.lower()}/liftOver/{chain_file_basename}"

diff --git a/setup.py b/setup.py
@@ -29,7 +29,7 @@ def walk_and_add(d, pkg_files):
 walk_and_add("cravat", cravat_files)
 setup(
     name="oakvar",
-    version="2.9.75",
+    version="2.9.76",
     description="A genomic variant analysis platform",
     long_description=long_description,
     long_description_content_type="text/x-rst",