Change typing approach

easyliftover/lifters/abstract.py

@@ -11,15 +11,17 @@ def __init__(self, from_ga: str, to_ga: str):
         """Initializes the lifter."""
         self.lo = LiftOver(from_ga, to_ga)
 
-    def convert_coordinate(self, chromosome: str, position: int) -> "Tuple[str, int] | None":
+    def convert_coordinate(
+        self, chromosome: str, position: int
+    ) -> "Tuple[str, int] | None":
         lifted = self.lo.convert_coordinate(chromosome, position)
-        
+
         if lifted is None:
             return None
-        
+
         if len(lifted) == 0:
             return None
-        
+
         return lifted[0][0], lifted[0][1]
 
     def convert_region(
@@ -35,13 +37,15 @@ def convert_region(
         if lifted_start is None or lifted_end is None:
             print(f"Could not lift {chromosome}:{start}-{end}")
             return None
-        
+
         if lifted_start[0] != lifted_end[0]:
             print(f"Chromosome changed from {chromosome} to {lifted_start[0]}")
             return None
-        
+
         if lifted_start[1] >= lifted_end[1]:
-            print(f"Start position {lifted_start[1]} is larger than end position {lifted_end[1]}")
+            print(
+                f"Start position {lifted_start[1]} is larger than end position {lifted_end[1]}"
+            )
             return None
 
         return lifted_start[0], lifted_start[1], lifted_end[1]
@@ -55,26 +59,33 @@ def lift_path(self, path: str) -> str:
     def lift_url(self, url: str) -> str:
         """Lifts a URL."""
         raise NotImplementedError
-
+
+    @staticmethod
+    @abstractmethod
+    def supported_formats() -> list:
+        """Returns the supported formats."""
+        raise NotImplementedError
+
+
 class AbstractTextLifter(AbstractLifter):
     """Abstract class for lifters of text-based files."""
-    
+
     @abstractmethod
     def lift_content(self, content: str) -> str:
         """Lifts the content of a file."""
         raise NotImplementedError
-    
+
     def lift_path(self, path: str) -> str:
         """Lifts a path."""
         with open(path) as f:
             content = f.read()
-        
+
         return self.lift_content(content)
-    
+
     def lift_url(self, url: str) -> str:
         """Lifts a URL."""
         response = requests.get(url)
-        
+
         return self.lift_content(response.text)
 
 

easyliftover/lifters/bed.py

@@ -24,3 +24,8 @@ def __lift_row__(self, row: str) -> "str | None":
             )
         else:
             return None
+
+    @staticmethod
+    def supported_formats() -> list:
+        """Returns the supported formats."""
+        return ["bed"]

easyliftover/lifters/bedgraph.py

@@ -24,3 +24,8 @@ def __lift_row__(self, row: str) -> "str | None":
             )
         else:
             return None
+
+    @staticmethod
+    def supported_formats() -> list:
+        """Returns the supported formats."""
+        return ["bedgraph", "bg"]

easyliftover/lifters/bigwig.py

@@ -46,3 +46,8 @@ def lift_bw(self, bw) -> str:
                     wig += f"{lifted_start}\t{rounded_value}\n"
 
         return wig
+
+    @staticmethod
+    def supported_formats() -> list:
+        """Returns the supported formats."""
+        return ["bigwig", "bw"]

easyliftover/lifters/gff.py

@@ -24,3 +24,8 @@ def __lift_row__(self, row: str) -> "str | None":
 
         else:
             return None
+
+    @staticmethod
+    def supported_formats() -> list:
+        """Returns the supported formats."""
+        return ["gff", "gff3", "gtf"]

easyliftover/lifters/vcf.py

@@ -23,3 +23,8 @@ def __lift_row__(self, row: str) -> "str | None":
             )
         else:
             return None
+
+    @staticmethod
+    def supported_formats() -> list:
+        """Returns the supported formats."""
+        return ["vcf"]

easyliftover/lifters/wig.py

@@ -60,3 +60,8 @@ def lift_content(self, content: str) -> str:
                 result.append(line)
 
         return "\n".join(result)
+
+    @staticmethod
+    def supported_formats() -> list:
+        """Returns the supported formats."""
+        return ["wig"]

easyliftover/liftover.py

@@ -1,37 +1,46 @@
-from .lifters import BedLifter, GffLifter, WigLifter, AbstractLifter, BigWigLifter, BedGraphLifter, VcfLifter
+from .lifters import (
+    BedLifter,
+    GffLifter,
+    WigLifter,
+    AbstractLifter,
+    BigWigLifter,
+    BedGraphLifter,
+    VcfLifter,
+)
 
-def get_lifter(fromGenome: str, toGenome: str, source: str, file_type: "str | None" = None) -> AbstractLifter:
+lifters = [BedLifter, GffLifter, WigLifter, BigWigLifter, BedGraphLifter, VcfLifter]
+
+def get_lifter(
+    fromGenome: str, toGenome: str, source: str, file_type: "str | None" = None
+) -> AbstractLifter:
     def get_class(c_type):
-        if c_type == "bed":
-            return BedLifter
-        elif c_type in ["gff", "gff3", "gtf"]:
-            return GffLifter
-        elif c_type == "wig":
-            return WigLifter
-        elif c_type == "bw" or c_type == "bigwig":
-            return BigWigLifter
-        elif c_type == "bedgraph" or c_type == "bg":
-            return BedGraphLifter
-        elif c_type == "vcf":
-            return VcfLifter
-        else:
-            raise Exception("Unsupported file type")
-
+        for lifter in lifters:
+            if c_type in lifter.supported_formats():
+                return lifter
+            raise Exception("Unsupported file type: " + c_type)
+
     def __get_type(path: str) -> str:
         return path.split(".")[-1]
-        
+
     chosen_type = file_type if file_type is not None else __get_type(source)
-
-    return get_class(chosen_type.lower())(fromGenome, toGenome)
+
+    clazz = get_class(chosen_type.lower())
+
+    if clazz is None:
+        raise Exception("Unsupported file type")
+
+    return clazz(fromGenome, toGenome)
+
 
 def liftover_url(
     fromGenome: str, toGenome: str, url: str, file_type: "str | None" = None
 ) -> str:
-    
+
     lifter = get_lifter(fromGenome, toGenome, url, file_type)
-    
+
     return lifter.lift_url(url)
 
+
 def liftover_path(
     fromGenome: str, toGenome: str, path: str, file_type: "str | None" = None
 ) -> str:

easyliftover/types.py

@@ -1,11 +1,4 @@
-import json
-import os
+from .liftover import lifters
 
 def get_file_types():
-    file_name = "types.json"
-
-    script_dir = os.path.dirname(__file__)
-
-    json_object = json.load(open(os.path.join(script_dir, file_name), "r"))
-
-    return json_object
+    return [format for lifter in lifters for format in lifter.supported_formats()]

test/test_lifters.py

@@ -1,32 +1,47 @@
 from easyliftover import *
 
-def __test__(clazz, assembly1: str, assembly2: str, path_assembly1: str, path_assembly2: str):
+
+def __test__(
+    clazz, assembly1: str, assembly2: str, path_assembly1: str, path_assembly2: str
+):
     content_assembly1 = open(path_assembly1).read()
     content_assembly2 = open(path_assembly2).read()
-    
+
     lifter: AbstractLifter = clazz(assembly1, assembly2)
     reversed_lifter: AbstractLifter = clazz(assembly2, assembly1)
 
     assert lifter.lift_path(path_assembly1) == content_assembly2
     assert reversed_lifter.lift_path(path_assembly2) == content_assembly1
 
+
 def test_bed():
-    __test__(BedLifter, 'hg19', 'hg38', 'test/data/hg19.bed', 'test/data/hg38.bed')
-
+    __test__(BedLifter, "hg19", "hg38", "test/data/hg19.bed", "test/data/hg38.bed")
+
+
 def test_vcf():
-    __test__(VcfLifter, 'hg19', 'hg38', 'test/data/hg19.vcf', 'test/data/hg38.vcf')
-
+    __test__(VcfLifter, "hg19", "hg38", "test/data/hg19.vcf", "test/data/hg38.vcf")
+
+
 def test_gff():
-    __test__(GffLifter, 'hg19', 'hg38', 'test/data/hg19.gff', 'test/data/hg38.gff')
-
+    __test__(GffLifter, "hg19", "hg38", "test/data/hg19.gff", "test/data/hg38.gff")
+
+
 def test_wig():
-    __test__(WigLifter, 'hg19', 'hg38', 'test/data/hg19.wig', 'test/data/hg38.wig')
-
+    __test__(WigLifter, "hg19", "hg38", "test/data/hg19.wig", "test/data/hg38.wig")
+
+
 def test_bedgraph():
-    __test__(BedGraphLifter, 'hg19', 'hg38', 'test/data/hg19.bedgraph', 'test/data/hg38.bedgraph')
+    __test__(
+        BedGraphLifter,
+        "hg19",
+        "hg38",
+        "test/data/hg19.bedgraph",
+        "test/data/hg38.bedgraph",
+    )
+
 
-#def test_bigwig():
+# def test_bigwig():
 #    lifter = BigWigLifter('hg38', 'hg19')
-#    
+#
 #    assert lifter.lift_url('https://github.com/deeptools/pyBigWig/raw/master/pyBigWigTest/test.bw') == ""
-#    assert lifter.lift_path('test/data/hg38.bw') == ""
+#    assert lifter.lift_path('test/data/hg38.bw') == ""

test/test_types.py

@@ -1,6 +1,9 @@
 from easyliftover.types import get_file_types
 
+
 def test_get_file_types():
     types = get_file_types()
-
-    assert len(types) > 0
+
+    expected = ["bed", "gff"]
+
+    assert all([t in types for t in expected])