weirdo 2.1.0__py3-none-any.whl

weirdo/data_manager.py

@@ -0,0 +1,475 @@
+"""Data management for WEIRDO reference data.
+
+Handles downloading and caching of reference data files.
+Data is stored in ~/.weirdo/ by default.
+
+Example
+-------
+>>> from weirdo.data_manager import DataManager
+>>> dm = DataManager()
+>>> dm.download('swissprot-8mers')  # Download reference data
+>>> dm.status()  # Show what's downloaded
+>>> dm.clear_all()  # Remove all data
+"""
+
+import json
+import os
+import shutil
+import sys
+import tempfile
+from datetime import datetime
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+from urllib.request import urlretrieve
+from urllib.error import URLError
+
+
+# Default data directory
+DEFAULT_DATA_DIR = Path.home() / '.weirdo'
+
+# Available datasets with their metadata
+DATASETS = {
+    'swissprot-8mers': {
+        'description': 'SwissProt 8-mer reference data (~100M k-mers)',
+        'url': 'https://github.com/pirl-unc/weirdo-data/releases/download/v1.0/swissprot-8mers.csv.gz',
+        'filename': 'swissprot-8mers.csv',
+        'compressed': True,
+        'size_mb': 2500,  # Compressed size
+        'uncompressed_size_mb': 7500,
+        'sha256': None,  # Will be verified if provided
+    },
+}
+
+
+
+def _progress_hook(block_num: int, block_size: int, total_size: int) -> None:
+    """Progress callback for urlretrieve."""
+    if total_size > 0:
+        downloaded = block_num * block_size
+        percent = min(100, downloaded * 100 / total_size)
+        mb_downloaded = downloaded / (1024 * 1024)
+        mb_total = total_size / (1024 * 1024)
+        sys.stdout.write(f'\r  Downloading: {percent:.1f}% ({mb_downloaded:.1f}/{mb_total:.1f} MB)')
+        sys.stdout.flush()
+    else:
+        downloaded = block_num * block_size
+        mb_downloaded = downloaded / (1024 * 1024)
+        sys.stdout.write(f'\r  Downloading: {mb_downloaded:.1f} MB')
+        sys.stdout.flush()
+
+
+class DataManager:
+    """Manages WEIRDO reference data.
+
+    Parameters
+    ----------
+    data_dir : str or Path, optional
+        Directory for storing data. Defaults to ~/.weirdo/
+    auto_download : bool, default=False
+        If True, automatically download missing data when needed.
+    verbose : bool, default=True
+        Print status messages.
+
+    Example
+    -------
+    >>> dm = DataManager()
+    >>> dm.download('swissprot-8mers')
+    >>> print(dm.status())
+    """
+
+    def __init__(
+        self,
+        data_dir: Optional[Path] = None,
+        auto_download: bool = False,
+        verbose: bool = True,
+    ):
+        self.data_dir = Path(data_dir) if data_dir else DEFAULT_DATA_DIR
+        self.auto_download = auto_download
+        self.verbose = verbose
+
+        # Subdirectories
+        self.downloads_dir = self.data_dir / 'downloads'
+        self.metadata_file = self.data_dir / 'metadata.json'
+
+        # Ensure directories exist
+        self._ensure_dirs()
+
+        # Load metadata
+        self._metadata = self._load_metadata()
+
+    def _ensure_dirs(self) -> None:
+        """Create data directories if they don't exist."""
+        self.data_dir.mkdir(parents=True, exist_ok=True)
+        self.downloads_dir.mkdir(exist_ok=True)
+
+    def _load_metadata(self) -> Dict[str, Any]:
+        """Load metadata from disk."""
+        if self.metadata_file.exists():
+            with open(self.metadata_file, 'r') as f:
+                data = json.load(f)
+            if 'downloads' not in data:
+                data['downloads'] = {}
+            return data
+        return {'downloads': {}}
+
+    def _save_metadata(self) -> None:
+        """Save metadata to disk."""
+        with open(self.metadata_file, 'w') as f:
+            json.dump(self._metadata, f, indent=2, default=str)
+
+    def _log(self, msg: str) -> None:
+        """Print message if verbose."""
+        if self.verbose:
+            print(msg)
+
+    # -------------------------------------------------------------------------
+    # Dataset queries
+    # -------------------------------------------------------------------------
+
+    def list_available_datasets(self) -> List[str]:
+        """List available datasets that can be downloaded.
+
+        Returns
+        -------
+        datasets : list of str
+            Names of available datasets.
+        """
+        return list(DATASETS.keys())
+
+    def get_dataset_info(self, name: str) -> Dict[str, Any]:
+        """Get information about a dataset.
+
+        Parameters
+        ----------
+        name : str
+            Dataset name.
+
+        Returns
+        -------
+        info : dict
+            Dataset metadata.
+        """
+        if name not in DATASETS:
+            raise ValueError(f"Unknown dataset: {name}. Available: {list(DATASETS.keys())}")
+        return DATASETS[name].copy()
+
+    # -------------------------------------------------------------------------
+    # Download management
+    # -------------------------------------------------------------------------
+
+    def is_downloaded(self, name: str) -> bool:
+        """Check if a dataset is downloaded.
+
+        Parameters
+        ----------
+        name : str
+            Dataset name.
+
+        Returns
+        -------
+        downloaded : bool
+            True if dataset is downloaded.
+        """
+        if name not in DATASETS:
+            raise ValueError(f"Unknown dataset: {name}")
+
+        filepath = self.downloads_dir / DATASETS[name]['filename']
+        return filepath.exists() and name in self._metadata.get('downloads', {})
+
+    def get_data_path(self, name: str, auto_download: Optional[bool] = None) -> Path:
+        """Get path to a dataset, optionally downloading if missing.
+
+        Parameters
+        ----------
+        name : str
+            Dataset name.
+        auto_download : bool, optional
+            Override instance auto_download setting.
+
+        Returns
+        -------
+        path : Path
+            Path to the dataset file.
+
+        Raises
+        ------
+        FileNotFoundError
+            If dataset is not downloaded and auto_download is False.
+        """
+        if name not in DATASETS:
+            raise ValueError(f"Unknown dataset: {name}")
+
+        filepath = self.downloads_dir / DATASETS[name]['filename']
+
+        if not filepath.exists():
+            should_download = auto_download if auto_download is not None else self.auto_download
+            if should_download:
+                self.download(name)
+            else:
+                raise FileNotFoundError(
+                    f"Dataset '{name}' not found. Run: weirdo data download {name}\n"
+                    f"Or use DataManager(auto_download=True)"
+                )
+
+        return filepath
+
+    def download(self, name: str, force: bool = False) -> Path:
+        """Download a dataset.
+
+        Parameters
+        ----------
+        name : str
+            Dataset name.
+        force : bool, default=False
+            Re-download even if already present.
+
+        Returns
+        -------
+        path : Path
+            Path to downloaded file.
+        """
+        if name not in DATASETS:
+            raise ValueError(f"Unknown dataset: {name}. Available: {list(DATASETS.keys())}")
+
+        info = DATASETS[name]
+        filepath = self.downloads_dir / info['filename']
+
+        if filepath.exists() and not force:
+            self._log(f"Dataset '{name}' already downloaded at {filepath}")
+            return filepath
+
+        self._log(f"Downloading '{name}'...")
+        self._log(f"  Source: {info['url']}")
+        self._log(f"  Size: ~{info['size_mb']} MB (compressed)")
+
+        # Download to temp file first
+        temp_path = None
+        try:
+            if info.get('compressed', False):
+                # Download compressed file
+                temp_fd, temp_path = tempfile.mkstemp(suffix='.gz')
+                os.close(temp_fd)
+                urlretrieve(info['url'], temp_path, _progress_hook)
+                print()  # Newline after progress
+
+                # Decompress
+                self._log("  Decompressing...")
+                import gzip
+                with gzip.open(temp_path, 'rb') as f_in:
+                    with open(filepath, 'wb') as f_out:
+                        shutil.copyfileobj(f_in, f_out)
+                os.unlink(temp_path)
+            else:
+                urlretrieve(info['url'], filepath, _progress_hook)
+                print()  # Newline after progress
+
+            # Update metadata
+            self._metadata.setdefault('downloads', {})[name] = {
+                'path': str(filepath),
+                'downloaded_at': datetime.now().isoformat(),
+                'size_bytes': filepath.stat().st_size,
+            }
+            self._save_metadata()
+
+            self._log(f"  Downloaded to: {filepath}")
+            return filepath
+
+        except URLError as e:
+            if temp_path and os.path.exists(temp_path):
+                os.unlink(temp_path)
+            raise RuntimeError(f"Failed to download '{name}': {e}")
+
+    def download_all(self, force: bool = False) -> List[Path]:
+        """Download all available datasets.
+
+        Parameters
+        ----------
+        force : bool, default=False
+            Re-download even if already present.
+
+        Returns
+        -------
+        paths : list of Path
+            Paths to downloaded files.
+        """
+        paths = []
+        for name in DATASETS:
+            paths.append(self.download(name, force=force))
+        return paths
+
+    def delete_download(self, name: str) -> bool:
+        """Delete a downloaded dataset.
+
+        Parameters
+        ----------
+        name : str
+            Dataset name.
+
+        Returns
+        -------
+        deleted : bool
+            True if file was deleted.
+        """
+        if name not in DATASETS:
+            raise ValueError(f"Unknown dataset: {name}")
+
+        filepath = self.downloads_dir / DATASETS[name]['filename']
+        deleted = False
+
+        if filepath.exists():
+            filepath.unlink()
+            deleted = True
+            self._log(f"Deleted: {filepath}")
+
+        if name in self._metadata.get('downloads', {}):
+            del self._metadata['downloads'][name]
+            self._save_metadata()
+
+        return deleted
+
+    def delete_all_downloads(self) -> int:
+        """Delete all downloaded datasets.
+
+        Returns
+        -------
+        count : int
+            Number of files deleted.
+        """
+        count = 0
+        for name in list(DATASETS.keys()):
+            if self.delete_download(name):
+                count += 1
+        return count
+
+    # -------------------------------------------------------------------------
+    # Status and cleanup
+    # -------------------------------------------------------------------------
+
+    def status(self) -> Dict[str, Any]:
+        """Get status of all downloaded data.
+
+        Returns
+        -------
+        status : dict
+            Status information.
+        """
+        status = {
+            'data_dir': str(self.data_dir),
+            'downloads': {},
+            'total_size_bytes': 0,
+        }
+
+        for name in DATASETS:
+            filepath = self.downloads_dir / DATASETS[name]['filename']
+            if filepath.exists():
+                size = filepath.stat().st_size
+                status['downloads'][name] = {
+                    'path': str(filepath),
+                    'size_bytes': size,
+                    'size_mb': size / (1024 * 1024),
+                    'metadata': self._metadata.get('downloads', {}).get(name, {}),
+                }
+                status['total_size_bytes'] += size
+            else:
+                status['downloads'][name] = {'downloaded': False}
+
+        status['total_size_mb'] = status['total_size_bytes'] / (1024 * 1024)
+        return status
+
+    def print_status(self) -> None:
+        """Print human-readable status."""
+        status = self.status()
+
+        print(f"\nWEIRDO Data Directory: {status['data_dir']}")
+        print(f"Total Disk Usage: {status['total_size_mb']:.1f} MB")
+
+        print("\nDatasets:")
+        print("-" * 70)
+        for name, info in status['downloads'].items():
+            ds_info = DATASETS.get(name, {})
+            if info.get('downloaded', True) and 'size_mb' in info:
+                meta = info.get('metadata', {})
+                downloaded_at = meta.get('downloaded_at', 'unknown')[:10]  # Just date
+                print(f"  [x] {name}")
+                print(f"      {ds_info.get('description', '')}")
+                print(f"      Status: Downloaded ({info['size_mb']:.0f} MB, {downloaded_at})")
+            else:
+                print(f"  [ ] {name}")
+                print(f"      {ds_info.get('description', '')}")
+                print(f"      Status: Not downloaded (~{ds_info.get('size_mb', '?')} MB compressed)")
+
+        print()
+
+    def clear_all(self) -> int:
+        """Delete all downloaded data.
+
+        Returns
+        -------
+        count : int
+            Number of downloads deleted.
+        """
+        return self.delete_all_downloads()
+
+    def disk_usage(self) -> int:
+        """Get total disk usage in bytes.
+
+        Returns
+        -------
+        bytes : int
+            Total disk usage.
+        """
+        return self.status()['total_size_bytes']
+
+
+# Singleton instance for convenience
+_default_manager: Optional[DataManager] = None
+
+
+def get_data_manager(
+    data_dir: Optional[Path] = None,
+    auto_download: bool = False,
+    verbose: bool = True,
+) -> DataManager:
+    """Get the default DataManager instance.
+
+    Parameters
+    ----------
+    data_dir : Path, optional
+        Override data directory.
+    auto_download : bool, default=False
+        Enable auto-download.
+    verbose : bool, default=True
+        Print status messages.
+
+    Returns
+    -------
+    manager : DataManager
+        Data manager instance.
+    """
+    global _default_manager
+
+    if _default_manager is None or data_dir is not None:
+        _default_manager = DataManager(
+            data_dir=data_dir,
+            auto_download=auto_download,
+            verbose=verbose,
+        )
+
+    return _default_manager
+
+
+def ensure_data_available(auto_download: bool = False) -> Path:
+    """Ensure reference data is available, optionally downloading.
+
+    Parameters
+    ----------
+    auto_download : bool, default=False
+        Download if not present.
+
+    Returns
+    -------
+    path : Path
+        Path to reference data.
+    """
+    dm = get_data_manager(auto_download=auto_download)
+    return dm.get_data_path('swissprot-8mers')

weirdo/distances.py

@@ -0,0 +1,16 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+def hamming(p1, p2):
+    n = min(len(p1), len(p2))
+    return sum([p1[i] != p2[i] for i in range(n)])
+

weirdo/matrices/BLOSUM30

@@ -0,0 +1,25 @@
+   A  B  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  V  W  X  Y  Z  * 
+A  4  0 -3  0  0 -2  0 -2  0  0 -1  1  0 -1  1 -1  1  1  1 -5  0 -4  0 -7 
+B  0  5 -2  5  0 -3  0 -2 -2  0 -1 -2  4 -2 -1 -2  0  0 -2 -5 -1 -3  0 -7 
+C -3 -2 17 -3  1 -3 -4 -5 -2 -3  0 -2 -1 -3 -2 -2 -2 -2 -2 -2 -2 -6  0 -7 
+D  0  5 -3  9  1 -5 -1 -2 -4  0 -1 -3  1 -1 -1 -1  0 -1 -2 -4 -1 -1  0 -7 
+E  0  0  1  1  6 -4 -2  0 -3  2 -1 -1 -1  1  2 -1  0 -2 -3 -1 -1 -2  5 -7 
+F -2 -3 -3 -5 -4 10 -3 -3  0 -1  2 -2 -1 -4 -3 -1 -1 -2  1  1 -1  3 -4 -7 
+G  0  0 -4 -1 -2 -3  8 -3 -1 -1 -2 -2  0 -1 -2 -2  0 -2 -3  1 -1 -3 -2 -7 
+H -2 -2 -5 -2  0 -3 -3 14 -2 -2 -1  2 -1  1  0 -1 -1 -2 -3 -5 -1  0  0 -7 
+I  0 -2 -2 -4 -3  0 -1 -2  6 -2  2  1  0 -3 -2 -3 -1  0  4 -3  0 -1 -3 -7 
+K  0  0 -3  0  2 -1 -1 -2 -2  4 -2  2  0  1  0  1  0 -1 -2 -2  0 -1  1 -7 
+L -1 -1  0 -1 -1  2 -2 -1  2 -2  4  2 -2 -3 -2 -2 -2  0  1 -2  0  3 -1 -7 
+M  1 -2 -2 -3 -1 -2 -2  2  1  2  2  6  0 -4 -1  0 -2  0  0 -3  0 -1 -1 -7 
+N  0  4 -1  1 -1 -1  0 -1  0  0 -2  0  8 -3 -1 -2  0  1 -2 -7  0 -4 -1 -7 
+P -1 -2 -3 -1  1 -4 -1  1 -3  1 -3 -4 -3 11  0 -1 -1  0 -4 -3 -1 -2  0 -7 
+Q  1 -1 -2 -1  2 -3 -2  0 -2  0 -2 -1 -1  0  8  3 -1  0 -3 -1  0 -1  4 -7 
+R -1 -2 -2 -1 -1 -1 -2 -1 -3  1 -2  0 -2 -1  3  8 -1 -3 -1  0 -1  0  0 -7 
+S  1  0 -2  0  0 -1  0 -1 -1  0 -2 -2  0 -1 -1 -1  4  2 -1 -3  0 -2 -1 -7 
+T  1  0 -2 -1 -2 -2 -2 -2  0 -1  0  0  1  0  0 -3  2  5  1 -5  0 -1 -1 -7 
+V  1 -2 -2 -2 -3  1 -3 -3  4 -2  1  0 -2 -4 -3 -1 -1  1  5 -3  0  1 -3 -7 
+W -5 -5 -2 -4 -1  1  1 -5 -3 -2 -2 -3 -7 -3 -1  0 -3 -5 -3 20 -2  5 -1 -7 
+X  0 -1 -2 -1 -1 -1 -1 -1  0  0  0  0  0 -1  0 -1  0  0  0 -2 -1 -1  0 -7 
+Y -4 -3 -6 -1 -2  3 -3  0 -1 -1  3 -1 -4 -2 -1  0 -2 -1  1  5 -1  9 -2 -7 
+Z  0  0  0  0  5 -4 -2  0 -3  1 -1 -1 -1  0  4  0 -1 -1 -3 -1  0 -2  4 -7 
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7  1 

weirdo/matrices/BLOSUM50

@@ -0,0 +1,21 @@
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V 
+A  5 -2 -1 -2 -1 -1 -1  0 -2 -1 -2 -1 -1 -3 -1  1  0 -3 -2  0
+R -2  7 -1 -2 -4  1  0 -3  0 -4 -3  3 -2 -3 -3 -1 -1 -3 -1 -3
+N -1 -1  7  2 -2  0  0  0  1 -3 -4  0 -2 -4 -2  1  0 -4 -2 -3
+D -2 -2  2  8 -4  0  2 -1 -1 -4 -4 -1 -4 -5 -1  0 -1 -5 -3 -4
+C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1
+Q -1  1  0  0 -3  7  2 -2  1 -3 -2  2  0 -4 -1  0 -1 -1 -1 -3
+E -1  0  0  2 -3  2  6 -3  0 -4 -3  1 -2 -3 -1 -1 -1 -3 -2 -3
+G  0 -3  0 -1 -3 -2 -3  8 -2 -4 -4 -2 -3 -4 -2  0 -2 -3 -3 -4
+H -2  0  1 -1 -3  1  0 -2 10 -4 -3  0 -1 -1 -2 -1 -2 -3  2 -4
+I -1 -4 -3 -4 -2 -3 -4 -4 -4  5  2 -3  2  0 -3 -3 -1 -3 -1  4
+L -2 -3 -4 -4 -2 -2 -3 -4 -3  2  5 -3  3  1 -4 -3 -1 -2 -1  1
+K -1  3  0 -1 -3  2  1 -2  0 -3 -3  6 -2 -4 -1  0 -1 -3 -2 -3
+M -1 -2 -2 -4 -2  0 -2 -3 -1  2  3 -2  7  0 -3 -2 -1 -1  0  1
+F -3 -3 -4 -5 -2 -4 -3 -4 -1  0  1 -4  0  8 -4 -3 -2  1  4 -1
+P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3
+S  1 -1  1  0 -1  0 -1  0 -1 -3 -3  0 -2 -3 -1  5  2 -4 -2 -2
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  2  5 -3 -2  0
+W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1  1 -4 -4 -4 15  2 -3
+Y -2 -1 -2 -3 -3 -1 -2 -3  2 -1 -1 -2  0  4 -3 -2 -2  2  8 -1
+V  0 -3 -3 -4 -1 -3 -3 -4 -4  4  1 -3  1 -1 -3 -2  0 -3 -1  5

weirdo/matrices/BLOSUM62

@@ -0,0 +1,27 @@
+# Entries for the BLOSUM62 matrix at a scale of ln(2)/2.0.
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  J  Z  X  *
+A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1 -1 -1 -4
+R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1 -2  0 -1 -4
+N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  4 -3  0 -1 -4
+D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4 -3  1 -1 -4
+C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -1 -3 -1 -4
+Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0 -2  4 -1 -4
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1 -3  4 -1 -4
+G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -4 -2 -1 -4
+H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0 -3  0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3  3 -3 -1 -4
+L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4  3 -3 -1 -4
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0 -3  1 -1 -4
+M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3  2 -1 -1 -4
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