Initial commit
This commit is contained in:
Zhongwei Li
378
skills/bioservices/scripts/compound_cross_reference.py
Executable file
378
skills/bioservices/scripts/compound_cross_reference.py
Executable file
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#!/usr/bin/env python3
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"""
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Compound Cross-Database Search
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This script searches for a compound by name and retrieves identifiers
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from multiple databases:
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- KEGG Compound
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- ChEBI
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- ChEMBL (via UniChem)
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- Basic compound properties
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Usage:
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python compound_cross_reference.py COMPOUND_NAME [--output FILE]
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Examples:
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python compound_cross_reference.py Geldanamycin
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python compound_cross_reference.py "Adenosine triphosphate"
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python compound_cross_reference.py Aspirin --output aspirin_info.txt
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"""
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import sys
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import argparse
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from bioservices import KEGG, UniChem, ChEBI, ChEMBL
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def search_kegg_compound(compound_name):
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"""Search KEGG for compound by name."""
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print(f"\n{'='*70}")
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print("STEP 1: KEGG Compound Search")
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print(f"{'='*70}")
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k = KEGG()
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print(f"Searching KEGG for: {compound_name}")
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try:
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results = k.find("compound", compound_name)
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if not results or not results.strip():
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print(f"✗ No results found in KEGG")
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return k, None
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# Parse results
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lines = results.strip().split("\n")
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print(f"✓ Found {len(lines)} result(s):\n")
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for i, line in enumerate(lines[:5], 1):
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parts = line.split("\t")
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kegg_id = parts[0]
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description = parts[1] if len(parts) > 1 else "No description"
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print(f" {i}. {kegg_id}: {description}")
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# Use first result
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first_result = lines[0].split("\t")
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kegg_id = first_result[0].replace("cpd:", "")
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print(f"\nUsing: {kegg_id}")
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return k, kegg_id
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except Exception as e:
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print(f"✗ Error: {e}")
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return k, None
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def get_kegg_info(kegg, kegg_id):
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"""Retrieve detailed KEGG compound information."""
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print(f"\n{'='*70}")
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print("STEP 2: KEGG Compound Details")
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print(f"{'='*70}")
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try:
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print(f"Retrieving KEGG entry for {kegg_id}...")
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entry = kegg.get(f"cpd:{kegg_id}")
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if not entry:
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print("✗ Failed to retrieve entry")
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return None
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# Parse entry
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compound_info = {
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'kegg_id': kegg_id,
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'name': None,
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'formula': None,
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'exact_mass': None,
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'mol_weight': None,
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'chebi_id': None,
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'pathways': []
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}
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current_section = None
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for line in entry.split("\n"):
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if line.startswith("NAME"):
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compound_info['name'] = line.replace("NAME", "").strip().rstrip(";")
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elif line.startswith("FORMULA"):
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compound_info['formula'] = line.replace("FORMULA", "").strip()
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elif line.startswith("EXACT_MASS"):
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compound_info['exact_mass'] = line.replace("EXACT_MASS", "").strip()
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elif line.startswith("MOL_WEIGHT"):
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compound_info['mol_weight'] = line.replace("MOL_WEIGHT", "").strip()
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elif "ChEBI:" in line:
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parts = line.split("ChEBI:")
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if len(parts) > 1:
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compound_info['chebi_id'] = parts[1].strip().split()[0]
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elif line.startswith("PATHWAY"):
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current_section = "pathway"
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pathway = line.replace("PATHWAY", "").strip()
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if pathway:
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compound_info['pathways'].append(pathway)
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elif current_section == "pathway" and line.startswith(" "):
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pathway = line.strip()
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if pathway:
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compound_info['pathways'].append(pathway)
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elif line.startswith(" ") and not line.startswith(" "):
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current_section = None
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# Display information
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print(f"\n✓ KEGG Compound Information:")
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print(f" ID: {compound_info['kegg_id']}")
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print(f" Name: {compound_info['name']}")
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print(f" Formula: {compound_info['formula']}")
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print(f" Exact Mass: {compound_info['exact_mass']}")
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print(f" Molecular Weight: {compound_info['mol_weight']}")
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if compound_info['chebi_id']:
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print(f" ChEBI ID: {compound_info['chebi_id']}")
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if compound_info['pathways']:
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print(f" Pathways: {len(compound_info['pathways'])} found")
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return compound_info
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except Exception as e:
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print(f"✗ Error: {e}")
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return None
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def get_chembl_id(kegg_id):
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"""Map KEGG ID to ChEMBL via UniChem."""
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print(f"\n{'='*70}")
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print("STEP 3: ChEMBL Mapping (via UniChem)")
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print(f"{'='*70}")
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try:
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u = UniChem()
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print(f"Mapping KEGG:{kegg_id} to ChEMBL...")
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chembl_id = u.get_compound_id_from_kegg(kegg_id)
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if chembl_id:
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print(f"✓ ChEMBL ID: {chembl_id}")
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return chembl_id
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else:
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print("✗ No ChEMBL mapping found")
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return None
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except Exception as e:
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print(f"✗ Error: {e}")
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return None
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def get_chebi_info(chebi_id):
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"""Retrieve ChEBI compound information."""
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print(f"\n{'='*70}")
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print("STEP 4: ChEBI Details")
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print(f"{'='*70}")
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if not chebi_id:
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print("⊘ No ChEBI ID available")
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return None
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try:
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c = ChEBI()
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print(f"Retrieving ChEBI entry for {chebi_id}...")
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# Ensure proper format
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if not chebi_id.startswith("CHEBI:"):
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chebi_id = f"CHEBI:{chebi_id}"
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entity = c.getCompleteEntity(chebi_id)
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if entity:
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print(f"\n✓ ChEBI Information:")
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print(f" ID: {entity.chebiId}")
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print(f" Name: {entity.chebiAsciiName}")
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if hasattr(entity, 'Formulae') and entity.Formulae:
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print(f" Formula: {entity.Formulae}")
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if hasattr(entity, 'mass') and entity.mass:
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print(f" Mass: {entity.mass}")
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if hasattr(entity, 'charge') and entity.charge:
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print(f" Charge: {entity.charge}")
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return {
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'chebi_id': entity.chebiId,
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'name': entity.chebiAsciiName,
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'formula': entity.Formulae if hasattr(entity, 'Formulae') else None,
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'mass': entity.mass if hasattr(entity, 'mass') else None
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}
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else:
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print("✗ Failed to retrieve ChEBI entry")
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return None
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except Exception as e:
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print(f"✗ Error: {e}")
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return None
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def get_chembl_info(chembl_id):
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"""Retrieve ChEMBL compound information."""
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print(f"\n{'='*70}")
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print("STEP 5: ChEMBL Details")
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print(f"{'='*70}")
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if not chembl_id:
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print("⊘ No ChEMBL ID available")
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return None
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try:
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c = ChEMBL()
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print(f"Retrieving ChEMBL entry for {chembl_id}...")
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compound = c.get_compound_by_chemblId(chembl_id)
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if compound:
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print(f"\n✓ ChEMBL Information:")
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print(f" ID: {chembl_id}")
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if 'pref_name' in compound and compound['pref_name']:
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print(f" Preferred Name: {compound['pref_name']}")
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if 'molecule_properties' in compound:
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props = compound['molecule_properties']
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if 'full_mwt' in props:
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print(f" Molecular Weight: {props['full_mwt']}")
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if 'alogp' in props:
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print(f" LogP: {props['alogp']}")
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if 'hba' in props:
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print(f" H-Bond Acceptors: {props['hba']}")
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if 'hbd' in props:
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print(f" H-Bond Donors: {props['hbd']}")
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if 'molecule_structures' in compound:
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structs = compound['molecule_structures']
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if 'canonical_smiles' in structs:
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smiles = structs['canonical_smiles']
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print(f" SMILES: {smiles[:60]}{'...' if len(smiles) > 60 else ''}")
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return compound
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else:
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print("✗ Failed to retrieve ChEMBL entry")
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return None
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except Exception as e:
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print(f"✗ Error: {e}")
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return None
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def save_results(compound_name, kegg_info, chembl_id, output_file):
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"""Save results to file."""
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print(f"\n{'='*70}")
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print(f"Saving results to {output_file}")
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print(f"{'='*70}")
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with open(output_file, 'w') as f:
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f.write("=" * 70 + "\n")
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f.write(f"Compound Cross-Reference Report: {compound_name}\n")
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f.write("=" * 70 + "\n\n")
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# KEGG information
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if kegg_info:
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f.write("KEGG Compound\n")
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f.write("-" * 70 + "\n")
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f.write(f"ID: {kegg_info['kegg_id']}\n")
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f.write(f"Name: {kegg_info['name']}\n")
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f.write(f"Formula: {kegg_info['formula']}\n")
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f.write(f"Exact Mass: {kegg_info['exact_mass']}\n")
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f.write(f"Molecular Weight: {kegg_info['mol_weight']}\n")
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f.write(f"Pathways: {len(kegg_info['pathways'])} found\n")
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f.write("\n")
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# Database IDs
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f.write("Cross-Database Identifiers\n")
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f.write("-" * 70 + "\n")
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if kegg_info:
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f.write(f"KEGG: {kegg_info['kegg_id']}\n")
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if kegg_info['chebi_id']:
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f.write(f"ChEBI: {kegg_info['chebi_id']}\n")
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if chembl_id:
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f.write(f"ChEMBL: {chembl_id}\n")
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f.write("\n")
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print(f"✓ Results saved")
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def main():
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"""Main workflow."""
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parser = argparse.ArgumentParser(
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description="Search compound across multiple databases",
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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python compound_cross_reference.py Geldanamycin
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python compound_cross_reference.py "Adenosine triphosphate"
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python compound_cross_reference.py Aspirin --output aspirin_info.txt
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"""
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)
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parser.add_argument("compound", help="Compound name to search")
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parser.add_argument("--output", default=None,
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help="Output file for results (optional)")
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args = parser.parse_args()
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print("=" * 70)
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print("BIOSERVICES: Compound Cross-Database Search")
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print("=" * 70)
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# Step 1: Search KEGG
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kegg, kegg_id = search_kegg_compound(args.compound)
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if not kegg_id:
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print("\n✗ Failed to find compound. Exiting.")
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sys.exit(1)
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# Step 2: Get KEGG details
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kegg_info = get_kegg_info(kegg, kegg_id)
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# Step 3: Map to ChEMBL
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chembl_id = get_chembl_id(kegg_id)
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# Step 4: Get ChEBI details
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chebi_info = None
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if kegg_info and kegg_info['chebi_id']:
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chebi_info = get_chebi_info(kegg_info['chebi_id'])
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# Step 5: Get ChEMBL details
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chembl_info = None
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if chembl_id:
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chembl_info = get_chembl_info(chembl_id)
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# Summary
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print(f"\n{'='*70}")
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print("SUMMARY")
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print(f"{'='*70}")
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print(f" Compound: {args.compound}")
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if kegg_info:
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print(f" KEGG ID: {kegg_info['kegg_id']}")
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if kegg_info['chebi_id']:
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print(f" ChEBI ID: {kegg_info['chebi_id']}")
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if chembl_id:
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print(f" ChEMBL ID: {chembl_id}")
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print(f"{'='*70}")
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# Save to file if requested
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if args.output:
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save_results(args.compound, kegg_info, chembl_id, args.output)
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if __name__ == "__main__":
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main()
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