bbmapy 0.0.2__py3-none-any.whl

bbmapy/__init__.py

@@ -0,0 +1,9 @@
+import os
+from bbmapy.scanner import scan_bbtools
+
+# Generate commands.py if it doesn't exist
+if not os.path.exists(os.path.join(os.path.dirname(__file__), "commands.py")):
+    scan_bbtools()
+
+# Import all functions from commands
+from bbmapy.commands import *

bbmapy/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.0.2'
+__version_tuple__ = version_tuple = (0, 0, 2)

bbmapy/base.py

@@ -0,0 +1,78 @@
+import os
+import sys
+import subprocess
+from typing import List, Dict, Union, Tuple
+from rich import print as rprint
+
+def find_bbtools_path():
+    # Check if we're running from an installed package
+    if getattr(sys, 'frozen', False):
+        # We're running from a bundle (e.g., PyInstaller)
+        base_path = sys._MEIPASS
+    else:
+        # We're running from a normal Python environment
+        base_path = os.path.abspath(os.path.dirname(__file__))
+    
+    # Navigate up to the project root
+    while not os.path.exists(os.path.join(base_path, 'vendor')):
+        base_path = os.path.dirname(base_path)
+        if base_path == os.path.dirname(base_path):  # We've reached the root directory
+            raise FileNotFoundError("Could not find BBTools directory")
+    
+    bbtools_path = os.path.join(base_path, 'vendor', 'bbmap')
+    
+    if not os.path.exists(bbtools_path):
+        raise FileNotFoundError(f"BBTools directory not found at {bbtools_path}")
+    
+    return bbtools_path
+
+BBTOOLS_PATH = find_bbtools_path()
+os.environ["PATH"] = f"{BBTOOLS_PATH}/current/:{os.environ["PATH"]}"
+
+def _pack_args(kwargs: Dict[str, Union[str, bool, int]]) -> List[str]:
+    args = []
+    
+    for key, value in kwargs.items():
+        if key in ['Xmx', 'Xms', 'da', 'ea', 'eoom']:
+            if isinstance(value, bool) and value:
+                args.append(f"-{key}")
+            elif value is not None:
+                args.append(f"-{key}{value}")
+        elif key == "in_file":
+            args.append(f"in={value}")
+        elif isinstance(value, bool) and value:
+            args.append(key)
+        elif value is not None:
+            args.append(f"{key}={value}")
+    
+    return args
+
+def _run_command(tool: str, args: List[str], capture_output: bool = False) -> Union[None, Tuple[str, str]]:
+    command = [os.path.join(BBTOOLS_PATH,tool)] + args # ,
+    # command = [tool] + args # ,
+
+    
+    if capture_output:
+        result = subprocess.run(command, capture_output=True, text=True)
+        if result.returncode != 0:
+            raise RuntimeError(f"Command failed: {' '.join(command)}\nError: {result.stderr}")
+        return result.stdout, result.stderr
+    else:
+        process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
+        
+        while True:
+            stdout_line = process.stdout.readline()
+            stderr_line = process.stderr.readline()
+            
+            if not stdout_line and not stderr_line and process.poll() is not None:
+                break
+            
+            if stdout_line:
+                rprint(stdout_line.strip())
+            if stderr_line:
+                rprint("[bold red]" + stderr_line.strip() + "[/bold red]")
+        
+        if process.returncode != 0:
+            raise RuntimeError(f"Command failed: {' '.join(command)}")
+        
+        return None