spymot 2.1.1.dev0__py3-none-any.whl

spymot/__init__.py

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+"""
+Spymot: Advanced Protein Motif Detection with AlphaFold Structural Validation
+
+A comprehensive protein analysis platform that combines motif detection with 3D structure 
+validation using AlphaFold2 confidence scores. Designed for cancer biology research, 
+drug discovery, and functional genomics.
+
+Version Information:
+- V1: Original foundational system with basic motif detection
+- V2: Enhanced production system with 94.6% motif coverage and advanced features
+
+Usage:
+    from spymot import analyze_sequence  # V1 functionality
+    from spymot.v2 import EnhancedSpymotAnalyzer  # V2 functionality
+    
+    # Basic analysis
+    result = analyze_sequence("p53", "MEEPQSDPSVEPPLSQETFSD...")
+    
+    # Enhanced analysis
+    analyzer = EnhancedSpymotAnalyzer()
+    result = analyzer.analyze_sequence_comprehensive("p53", "MEEPQSDPSVEPPLSQETFSD...")
+"""
+
+from ._version import __version__
+
+# V1 Imports (Original functionality)
+try:
+    from .v1.analyzer import analyze_sequence, analyze_by_pdb
+    from .v1.motifs import scan_motifs, get_motif_statistics
+    from .v1.targeting import predict_targeting
+    from .v1.afdb import get_prediction_meta, fetch_pdb_text, mean_plddt_over_region
+    from .v1.utils import read_fasta, validate_sequence
+    
+    __all_v1__ = [
+        "analyze_sequence",
+        "analyze_by_pdb", 
+        "scan_motifs",
+        "get_motif_statistics",
+        "predict_targeting",
+        "get_prediction_meta",
+        "fetch_pdb_text",
+        "mean_plddt_over_region",
+        "read_fasta",
+        "validate_sequence"
+    ]
+except ImportError:
+    __all_v1__ = []
+
+# V2 Imports (Enhanced functionality)
+try:
+    from .v2.enhanced_analyzer import EnhancedSpymotAnalyzer
+    from .v2.context_aware_detector import ContextAwareDetector
+    from .v2.enhanced_motifs_db import EnhancedMotifDatabase
+    
+    __all_v2__ = [
+        "EnhancedSpymotAnalyzer",
+        "ContextAwareDetector", 
+        "EnhancedMotifDatabase"
+    ]
+except ImportError:
+    __all_v2__ = []
+
+# Main exports (V1 for backward compatibility)
+__all__ = [
+    "__version__",
+    # V1 exports
+    "analyze_sequence",
+    "analyze_by_pdb",
+    "scan_motifs", 
+    "get_motif_statistics",
+    "predict_targeting",
+    "read_fasta",
+    "validate_sequence",
+    # V2 exports
+    "EnhancedSpymotAnalyzer",
+    "ContextAwareDetector",
+    "EnhancedMotifDatabase"
+]
+
+# Package metadata
+__author__ = "Erfan Zohrabi"
+__email__ = "erfanzohrabi.ez@gmail.com"
+__description__ = "Advanced Protein Motif Detection with AlphaFold Structural Validation"
+__url__ = "https://github.com/ErfanZohrabi/Spymot"
+__license__ = "MIT"
+
+# Version info
+def get_version():
+    """Get the current version of Spymot."""
+    return __version__
+
+def get_version_info():
+    """Get detailed version information."""
+    return {
+        "version": __version__,
+        "author": __author__,
+        "email": __email__,
+        "description": __description__,
+        "url": __url__,
+        "license": __license__,
+        "v1_available": len(__all_v1__) > 0,
+        "v2_available": len(__all_v2__) > 0
+    }

spymot/_version.py

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+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '2.1.1.dev0'
+__version_tuple__ = version_tuple = (2, 1, 1, 'dev0')
+
+__commit_id__ = commit_id = None

spymot/cli.py

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+"""
+Main command-line interface for Spymot package.
+Provides unified access to both V1 and V2 functionality.
+"""
+
+import click
+import sys
+from pathlib import Path
+from typing import Optional
+
+from ._version import __version__
+
+@click.group(context_settings={'help_option_names': ['-h', '--help']})
+@click.version_option(__version__, '-v', '--version')
+def main():
+    """
+    🧬 Spymot - Advanced Protein Motif Detection with AlphaFold Structural Validation
+    
+    A comprehensive protein analysis platform for cancer biology research, 
+    drug discovery, and functional genomics.
+    
+    Choose your version:
+    • V1: Original foundational system with basic motif detection
+    • V2: Enhanced production system with 94.6% motif coverage
+    
+    Examples:
+      spymot v1 analyze protein.fasta --format json
+      spymot v2 analyze protein.fasta --database all --cancer-only
+      spymot interactive
+    """
+    pass
+
+@main.group()
+def v1():
+    """V1: Original Spymot functionality (basic motif detection)"""
+    pass
+
+@main.group() 
+def v2():
+    """V2: Enhanced Spymot functionality (comprehensive analysis)"""
+    pass
+
+@main.command()
+@click.option('--version', 'version_choice', 
+              type=click.Choice(['v1', 'v2']), 
+              default='v2',
+              help='Choose Spymot version')
+def interactive(version_choice: str):
+    """Launch interactive analysis mode"""
+    try:
+        if version_choice == 'v1':
+            from .v1.cli import interactive as v1_interactive
+            v1_interactive()
+        else:
+            from .v2.scripts.interactive_cli import main as v2_interactive
+            v2_interactive()
+    except ImportError as e:
+        click.echo(f"❌ Error: {e}", err=True)
+        click.echo(f"Make sure {version_choice} is properly installed.", err=True)
+        sys.exit(1)
+
+@v1.command()
+@click.argument('input_file', type=click.Path(exists=True, path_type=Path))
+@click.option('--id', 'uniprot_id', help='UniProt ID hint for structure mapping')
+@click.option('-o', '--output', type=click.Path(path_type=Path), help='Output file path')
+@click.option('--format', 'output_format', default='json', 
+              type=click.Choice(['json', 'yaml', 'txt']), help='Output format')
+@click.option('--database', 'motif_db_type', default='all',
+              type=click.Choice(['all', 'cancer', 'signals', 'hardcoded']),
+              help='Which motif databases to use')
+@click.option('--verbose', '-v', is_flag=True, help='Verbose output')
+def analyze(input_file: Path, uniprot_id: Optional[str], output: Optional[Path],
+           output_format: str, motif_db_type: str, verbose: bool):
+    """Analyze protein sequence using V1 functionality"""
+    try:
+        from .v1.cli import analyze as v1_analyze
+        v1_analyze(input_file, uniprot_id, output, output_format, True, False, 0.0, motif_db_type, False, verbose)
+    except ImportError as e:
+        click.echo(f"❌ Error: V1 functionality not available: {e}", err=True)
+        sys.exit(1)
+
+@v1.command()
+@click.argument('pdb_id', type=str)
+@click.option('-o', '--output', type=click.Path(path_type=Path), help='Output file path')
+@click.option('--format', 'output_format', default='json',
+              type=click.Choice(['json', 'yaml', 'txt']), help='Output format')
+@click.option('--verbose', '-v', is_flag=True, help='Verbose output')
+def pdb(pdb_id: str, output: Optional[Path], output_format: str, verbose: bool):
+    """Analyze protein by PDB structure ID using V1 functionality"""
+    try:
+        from .v1.cli import pdb as v1_pdb
+        v1_pdb(pdb_id, output, output_format, verbose)
+    except ImportError as e:
+        click.echo(f"❌ Error: V1 functionality not available: {e}", err=True)
+        sys.exit(1)
+
+@v2.command()
+@click.argument('input_file', type=click.Path(exists=True, path_type=Path))
+@click.option('--id', 'uniprot_id', help='UniProt ID hint for structure mapping')
+@click.option('-o', '--output', type=click.Path(path_type=Path), help='Output file path')
+@click.option('--format', 'output_format', default='json',
+              type=click.Choice(['json', 'yaml', 'txt']), help='Output format')
+@click.option('--database', 'motif_db_type', default='all',
+              type=click.Choice(['all', 'cancer', 'signals', 'hardcoded']),
+              help='Which motif databases to use')
+@click.option('--cancer-only', is_flag=True, help='Show only cancer-relevant motifs')
+@click.option('--min-confidence', type=float, default=0.0,
+              help='Minimum confidence threshold (0.0-1.0)')
+@click.option('--verbose', '-v', is_flag=True, help='Verbose output')
+def analyze(input_file: Path, uniprot_id: Optional[str], output: Optional[Path],
+           output_format: str, motif_db_type: str, cancer_only: bool,
+           min_confidence: float, verbose: bool):
+    """Analyze protein sequence using V2 enhanced functionality"""
+    try:
+        from .v2.scripts.enhanced_cli import analyze as v2_analyze
+        v2_analyze(input_file, uniprot_id, output, output_format, motif_db_type, 
+                  cancer_only, min_confidence, verbose)
+    except ImportError as e:
+        click.echo(f"❌ Error: V2 functionality not available: {e}", err=True)
+        sys.exit(1)
+
+@v2.command()
+@click.option('--format', 'output_format', default='txt',
+              type=click.Choice(['json', 'yaml', 'txt']), help='Output format')
+@click.option('--verbose', '-v', is_flag=True, help='Verbose output')
+def databases(output_format: str, verbose: bool):
+    """Show information about available motif databases (V2)"""
+    try:
+        from .v2.scripts.enhanced_cli import databases as v2_databases
+        v2_databases(output_format, verbose)
+    except ImportError as e:
+        click.echo(f"❌ Error: V2 functionality not available: {e}", err=True)
+        sys.exit(1)
+
+@main.command()
+def info():
+    """Show package information and version details"""
+    from . import get_version_info
+    
+    info = get_version_info()
+    
+    click.echo("🧬 SPYMOT PACKAGE INFORMATION")
+    click.echo("=" * 50)
+    click.echo(f"Version: {info['version']}")
+    click.echo(f"Author: {info['author']}")
+    click.echo(f"Description: {info['description']}")
+    click.echo(f"License: {info['license']}")
+    click.echo(f"URL: {info['url']}")
+    click.echo()
+    click.echo("Available Components:")
+    click.echo(f"  • V1 (Original): {'✅ Available' if info['v1_available'] else '❌ Not Available'}")
+    click.echo(f"  • V2 (Enhanced): {'✅ Available' if info['v2_available'] else '❌ Not Available'}")
+    click.echo()
+    click.echo("Usage Examples:")
+    click.echo("  spymot v1 analyze protein.fasta --format json")
+    click.echo("  spymot v2 analyze protein.fasta --database all --cancer-only")
+    click.echo("  spymot interactive --version v2")
+
+if __name__ == '__main__':
+    main()

spymot/v1/__init__.py

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+"""
+Spymot V1: Original foundational protein motif detection system.
+
+This module provides access to the original Spymot functionality including:
+- Basic motif detection
+- AlphaFold integration
+- Simple CLI interface
+- Core motif database
+"""
+
+# Import V1 modules from the actual V1 directory
+import sys
+from pathlib import Path
+
+# Add V1 directory to path for imports
+v1_path = Path(__file__).parent.parent.parent.parent / "V1"
+if str(v1_path) not in sys.path:
+    sys.path.insert(0, str(v1_path))
+
+try:
+    # Import V1 modules
+    from spymot.analyzer import analyze_sequence, analyze_by_pdb
+    from spymot.motifs import scan_motifs, get_motif_statistics
+    from spymot.targeting import predict_targeting
+    from spymot.afdb import get_prediction_meta, fetch_pdb_text, mean_plddt_over_region
+    from spymot.utils import read_fasta, validate_sequence
+    from spymot.cli import main as cli_main, interactive
+    
+    __all__ = [
+        "analyze_sequence",
+        "analyze_by_pdb",
+        "scan_motifs", 
+        "get_motif_statistics",
+        "predict_targeting",
+        "get_prediction_meta",
+        "fetch_pdb_text",
+        "mean_plddt_over_region",
+        "read_fasta",
+        "validate_sequence",
+        "cli_main",
+        "interactive"
+    ]
+    
+    V1_AVAILABLE = True
+    
+except ImportError as e:
+    # V1 not available
+    __all__ = []
+    V1_AVAILABLE = False
+    V1_ERROR = str(e)

spymot/v1/cli.py

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+"""
+V1 CLI wrapper for original Spymot functionality.
+"""
+
+import sys
+from pathlib import Path
+
+# Add V1 directory to path
+v1_path = Path(__file__).parent.parent.parent.parent.parent / "V1"
+if str(v1_path) not in sys.path:
+    sys.path.insert(0, str(v1_path))
+
+def main():
+    """Main entry point for V1 CLI."""
+    try:
+        from spymot.cli import main as v1_main
+        v1_main()
+    except ImportError as e:
+        print(f"❌ Error: V1 CLI not available: {e}", file=sys.stderr)
+        sys.exit(1)
+
+def interactive():
+    """Interactive mode for V1."""
+    try:
+        from spymot.cli import interactive as v1_interactive
+        v1_interactive()
+    except ImportError as e:
+        print(f"❌ Error: V1 interactive mode not available: {e}", file=sys.stderr)
+        sys.exit(1)
+
+if __name__ == '__main__':
+    main()

spymot/v2/__init__.py

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+"""
+Spymot V2: Enhanced protein motif detection system.
+
+This module provides access to the enhanced Spymot functionality including:
+- 94.6% motif coverage (316+ patterns)
+- Context-aware detection
+- Advanced cancer relevance scoring
+- Rich JSON output with biological interpretation
+- Production-ready features
+"""
+
+# Import V2 modules from the actual V2 directory
+import sys
+from pathlib import Path
+
+# Add V2 directory to path for imports
+v2_path = Path(__file__).parent.parent.parent.parent / "V2"
+if str(v2_path) not in sys.path:
+    sys.path.insert(0, str(v2_path))
+
+try:
+    # Import V2 modules
+    from enhanced_analyzer import EnhancedSpymotAnalyzer
+    from context_aware_detector import ContextAwareDetector
+    from enhanced_motifs_db import EnhancedMotifDatabase
+    
+    # Import scripts
+    from scripts.enhanced_cli import main as enhanced_cli_main
+    from scripts.enhanced_demo import main as demo_main
+    from scripts.interactive_cli import main as interactive_main
+    
+    __all__ = [
+        "EnhancedSpymotAnalyzer",
+        "ContextAwareDetector",
+        "EnhancedMotifDatabase",
+        "enhanced_cli_main",
+        "demo_main", 
+        "interactive_main"
+    ]
+    
+    V2_AVAILABLE = True
+    
+except ImportError as e:
+    # V2 not available
+    __all__ = []
+    V2_AVAILABLE = False
+    V2_ERROR = str(e)

spymot/v2/scripts/__init__.py

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+"""
+Spymot V2 Scripts: Command-line interfaces for enhanced functionality.
+"""
+
+# This module provides access to V2 CLI scripts
+# The actual scripts are imported from the V2 directory

spymot/v2/scripts/enhanced_cli.py

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+"""
+Enhanced CLI wrapper for V2 functionality.
+"""
+
+import sys
+from pathlib import Path
+
+# Add V2 directory to path
+v2_path = Path(__file__).parent.parent.parent.parent.parent / "V2"
+if str(v2_path) not in sys.path:
+    sys.path.insert(0, str(v2_path))
+
+def main():
+    """Main entry point for enhanced CLI."""
+    try:
+        from scripts.enhanced_cli import main as v2_main
+        v2_main()
+    except ImportError as e:
+        print(f"❌ Error: V2 enhanced CLI not available: {e}", file=sys.stderr)
+        sys.exit(1)
+
+def analyze(input_file, uniprot_id=None, output=None, output_format='json', 
+           motif_db_type='all', cancer_only=False, min_confidence=0.0, verbose=False):
+    """Analyze protein sequence using V2 enhanced functionality."""
+    try:
+        from scripts.enhanced_cli import analyze as v2_analyze
+        v2_analyze(input_file, uniprot_id, output, output_format, motif_db_type,
+                  cancer_only, min_confidence, verbose)
+    except ImportError as e:
+        print(f"❌ Error: V2 enhanced analysis not available: {e}", file=sys.stderr)
+        sys.exit(1)
+
+def databases(output_format='txt', verbose=False):
+    """Show database information."""
+    try:
+        from scripts.enhanced_cli import databases as v2_databases
+        v2_databases(output_format, verbose)
+    except ImportError as e:
+        print(f"❌ Error: V2 database info not available: {e}", file=sys.stderr)
+        sys.exit(1)
+
+if __name__ == '__main__':
+    main()

spymot/v2/scripts/enhanced_demo.py

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+"""
+Enhanced demo wrapper for V2 functionality.
+"""
+
+import sys
+from pathlib import Path
+
+# Add V2 directory to path
+v2_path = Path(__file__).parent.parent.parent.parent.parent / "V2"
+if str(v2_path) not in sys.path:
+    sys.path.insert(0, str(v2_path))
+
+def main():
+    """Main entry point for enhanced demo."""
+    try:
+        from scripts.enhanced_demo import main as v2_demo
+        v2_demo()
+    except ImportError as e:
+        print(f"❌ Error: V2 enhanced demo not available: {e}", file=sys.stderr)
+        sys.exit(1)
+
+if __name__ == '__main__':
+    main()

spymot/v2/scripts/interactive_cli.py

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+"""
+Interactive CLI wrapper for V2 functionality.
+"""
+
+import sys
+from pathlib import Path
+
+# Add V2 directory to path
+v2_path = Path(__file__).parent.parent.parent.parent.parent / "V2"
+if str(v2_path) not in sys.path:
+    sys.path.insert(0, str(v2_path))
+
+def main():
+    """Main entry point for interactive CLI."""
+    try:
+        from scripts.interactive_cli import main as v2_interactive
+        v2_interactive()
+    except ImportError as e:
+        print(f"❌ Error: V2 interactive CLI not available: {e}", file=sys.stderr)
+        sys.exit(1)
+
+if __name__ == '__main__':
+    main()