Initial commit
This commit is contained in:
Zhongwei Li
408
skills/bioservices/scripts/protein_analysis_workflow.py
Executable file
408
skills/bioservices/scripts/protein_analysis_workflow.py
Executable file
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#!/usr/bin/env python3
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"""
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Complete Protein Analysis Workflow
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This script performs a comprehensive protein analysis pipeline:
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1. UniProt search and identifier retrieval
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2. FASTA sequence retrieval
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3. BLAST similarity search
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4. KEGG pathway discovery
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5. PSICQUIC interaction mapping
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6. GO annotation retrieval
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Usage:
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python protein_analysis_workflow.py PROTEIN_NAME EMAIL [--skip-blast]
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Examples:
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python protein_analysis_workflow.py ZAP70_HUMAN user@example.com
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python protein_analysis_workflow.py P43403 user@example.com --skip-blast
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Note: BLAST searches can take several minutes. Use --skip-blast to skip this step.
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"""
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import sys
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import time
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import argparse
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from bioservices import UniProt, KEGG, NCBIblast, PSICQUIC, QuickGO
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def search_protein(query):
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"""Search UniProt for protein and retrieve basic information."""
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print(f"\n{'='*70}")
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print("STEP 1: UniProt Search")
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print(f"{'='*70}")
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u = UniProt(verbose=False)
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print(f"Searching for: {query}")
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# Try direct retrieval first (if query looks like accession)
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if len(query) == 6 and query[0] in "OPQ":
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try:
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entry = u.retrieve(query, frmt="tab")
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if entry:
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uniprot_id = query
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print(f"✓ Found UniProt entry: {uniprot_id}")
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return u, uniprot_id
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except:
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pass
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# Otherwise search
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results = u.search(query, frmt="tab", columns="id,genes,organism,length,protein names", limit=5)
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if not results:
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print("✗ No results found")
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return u, None
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lines = results.strip().split("\n")
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if len(lines) < 2:
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print("✗ No entries found")
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return u, None
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# Display results
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print(f"\n✓ Found {len(lines)-1} result(s):")
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for i, line in enumerate(lines[1:], 1):
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fields = line.split("\t")
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print(f" {i}. {fields[0]} - {fields[1]} ({fields[2]})")
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# Use first result
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first_entry = lines[1].split("\t")
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uniprot_id = first_entry[0]
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gene_names = first_entry[1] if len(first_entry) > 1 else "N/A"
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organism = first_entry[2] if len(first_entry) > 2 else "N/A"
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length = first_entry[3] if len(first_entry) > 3 else "N/A"
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protein_name = first_entry[4] if len(first_entry) > 4 else "N/A"
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print(f"\nUsing first result:")
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print(f" UniProt ID: {uniprot_id}")
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print(f" Gene names: {gene_names}")
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print(f" Organism: {organism}")
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print(f" Length: {length} aa")
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print(f" Protein: {protein_name}")
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return u, uniprot_id
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def retrieve_sequence(uniprot, uniprot_id):
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"""Retrieve FASTA sequence for protein."""
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print(f"\n{'='*70}")
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print("STEP 2: FASTA Sequence Retrieval")
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print(f"{'='*70}")
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try:
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sequence = uniprot.retrieve(uniprot_id, frmt="fasta")
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if sequence:
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# Extract sequence only (remove header)
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lines = sequence.strip().split("\n")
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header = lines[0]
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seq_only = "".join(lines[1:])
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print(f"✓ Retrieved sequence:")
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print(f" Header: {header}")
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print(f" Length: {len(seq_only)} residues")
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print(f" First 60 residues: {seq_only[:60]}...")
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return seq_only
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else:
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print("✗ Failed to retrieve sequence")
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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 run_blast(sequence, email, skip=False):
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"""Run BLAST similarity search."""
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print(f"\n{'='*70}")
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print("STEP 3: BLAST Similarity Search")
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print(f"{'='*70}")
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if skip:
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print("⊘ Skipped (--skip-blast flag)")
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return None
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if not email or "@" not in email:
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print("⊘ Skipped (valid email required for BLAST)")
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return None
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try:
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print(f"Submitting BLASTP job...")
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print(f" Database: uniprotkb")
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print(f" Sequence length: {len(sequence)} aa")
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s = NCBIblast(verbose=False)
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jobid = s.run(
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program="blastp",
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sequence=sequence,
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stype="protein",
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database="uniprotkb",
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email=email
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)
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print(f"✓ Job submitted: {jobid}")
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print(f" Waiting for completion...")
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# Poll for completion
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max_wait = 300 # 5 minutes
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start_time = time.time()
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while time.time() - start_time < max_wait:
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status = s.getStatus(jobid)
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elapsed = int(time.time() - start_time)
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print(f" Status: {status} (elapsed: {elapsed}s)", end="\r")
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if status == "FINISHED":
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print(f"\n✓ BLAST completed in {elapsed}s")
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# Retrieve results
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results = s.getResult(jobid, "out")
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# Parse and display summary
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lines = results.split("\n")
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print(f"\n Results preview:")
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for line in lines[:20]:
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if line.strip():
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print(f" {line}")
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return results
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elif status == "ERROR":
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print(f"\n✗ BLAST job failed")
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return None
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time.sleep(5)
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print(f"\n✗ Timeout after {max_wait}s")
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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 discover_pathways(uniprot, kegg, uniprot_id):
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"""Discover KEGG pathways for protein."""
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print(f"\n{'='*70}")
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print("STEP 4: KEGG Pathway Discovery")
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print(f"{'='*70}")
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try:
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# Map UniProt → KEGG
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print(f"Mapping {uniprot_id} to KEGG...")
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kegg_mapping = uniprot.mapping(fr="UniProtKB_AC-ID", to="KEGG", query=uniprot_id)
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if not kegg_mapping or uniprot_id not in kegg_mapping:
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print("✗ No KEGG mapping found")
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return []
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kegg_ids = kegg_mapping[uniprot_id]
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print(f"✓ KEGG ID(s): {kegg_ids}")
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# Get pathways for first KEGG ID
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kegg_id = kegg_ids[0]
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organism, gene_id = kegg_id.split(":")
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print(f"\nSearching pathways for {kegg_id}...")
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pathways = kegg.get_pathway_by_gene(gene_id, organism)
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if not pathways:
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print("✗ No pathways found")
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return []
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print(f"✓ Found {len(pathways)} pathway(s):\n")
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# Get pathway names
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pathway_info = []
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for pathway_id in pathways:
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try:
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entry = kegg.get(pathway_id)
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# Extract pathway name
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pathway_name = "Unknown"
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for line in entry.split("\n"):
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if line.startswith("NAME"):
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pathway_name = line.replace("NAME", "").strip()
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break
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pathway_info.append((pathway_id, pathway_name))
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print(f" • {pathway_id}: {pathway_name}")
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except Exception as e:
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print(f" • {pathway_id}: [Error retrieving name]")
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return pathway_info
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except Exception as e:
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print(f"✗ Error: {e}")
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return []
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def find_interactions(protein_query):
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"""Find protein-protein interactions via PSICQUIC."""
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print(f"\n{'='*70}")
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print("STEP 5: Protein-Protein Interactions")
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print(f"{'='*70}")
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try:
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p = PSICQUIC()
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# Try querying MINT database
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query = f"{protein_query} AND species:9606"
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print(f"Querying MINT database...")
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print(f" Query: {query}")
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results = p.query("mint", query)
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if not results:
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print("✗ No interactions found in MINT")
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return []
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# Parse PSI-MI TAB format
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lines = results.strip().split("\n")
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print(f"✓ Found {len(lines)} interaction(s):\n")
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# Display first 10 interactions
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interactions = []
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for i, line in enumerate(lines[:10], 1):
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fields = line.split("\t")
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if len(fields) >= 12:
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protein_a = fields[4].split(":")[1] if ":" in fields[4] else fields[4]
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protein_b = fields[5].split(":")[1] if ":" in fields[5] else fields[5]
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interaction_type = fields[11]
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interactions.append((protein_a, protein_b, interaction_type))
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print(f" {i}. {protein_a} ↔ {protein_b}")
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if len(lines) > 10:
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print(f" ... and {len(lines)-10} more")
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return interactions
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except Exception as e:
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print(f"✗ Error: {e}")
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return []
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def get_go_annotations(uniprot_id):
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"""Retrieve GO annotations."""
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print(f"\n{'='*70}")
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print("STEP 6: Gene Ontology Annotations")
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print(f"{'='*70}")
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try:
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g = QuickGO()
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print(f"Retrieving GO annotations for {uniprot_id}...")
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annotations = g.Annotation(protein=uniprot_id, format="tsv")
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if not annotations:
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print("✗ No GO annotations found")
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return []
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lines = annotations.strip().split("\n")
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print(f"✓ Found {len(lines)-1} annotation(s)\n")
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# Group by aspect
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aspects = {"P": [], "F": [], "C": []}
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for line in lines[1:]:
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fields = line.split("\t")
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if len(fields) >= 9:
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go_id = fields[6]
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go_term = fields[7]
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go_aspect = fields[8]
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if go_aspect in aspects:
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aspects[go_aspect].append((go_id, go_term))
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# Display summary
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print(f" Biological Process (P): {len(aspects['P'])} terms")
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for go_id, go_term in aspects['P'][:5]:
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print(f" • {go_id}: {go_term}")
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if len(aspects['P']) > 5:
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print(f" ... and {len(aspects['P'])-5} more")
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print(f"\n Molecular Function (F): {len(aspects['F'])} terms")
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for go_id, go_term in aspects['F'][:5]:
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print(f" • {go_id}: {go_term}")
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if len(aspects['F']) > 5:
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print(f" ... and {len(aspects['F'])-5} more")
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print(f"\n Cellular Component (C): {len(aspects['C'])} terms")
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for go_id, go_term in aspects['C'][:5]:
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print(f" • {go_id}: {go_term}")
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if len(aspects['C']) > 5:
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print(f" ... and {len(aspects['C'])-5} more")
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return aspects
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except Exception as e:
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print(f"✗ Error: {e}")
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return {}
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def main():
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"""Main workflow."""
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parser = argparse.ArgumentParser(
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description="Complete protein analysis workflow using BioServices",
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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python protein_analysis_workflow.py ZAP70_HUMAN user@example.com
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python protein_analysis_workflow.py P43403 user@example.com --skip-blast
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"""
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)
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parser.add_argument("protein", help="Protein name or UniProt ID")
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parser.add_argument("email", help="Email address (required for BLAST)")
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parser.add_argument("--skip-blast", action="store_true",
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help="Skip BLAST search (faster)")
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args = parser.parse_args()
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print("=" * 70)
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print("BIOSERVICES: Complete Protein Analysis Workflow")
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print("=" * 70)
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# Step 1: Search protein
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uniprot, uniprot_id = search_protein(args.protein)
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if not uniprot_id:
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print("\n✗ Failed to find protein. Exiting.")
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sys.exit(1)
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# Step 2: Retrieve sequence
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sequence = retrieve_sequence(uniprot, uniprot_id)
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if not sequence:
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print("\n⚠ Warning: Could not retrieve sequence")
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# Step 3: BLAST search
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if sequence:
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blast_results = run_blast(sequence, args.email, args.skip_blast)
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# Step 4: Pathway discovery
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kegg = KEGG()
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pathways = discover_pathways(uniprot, kegg, uniprot_id)
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# Step 5: Interaction mapping
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interactions = find_interactions(args.protein)
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# Step 6: GO annotations
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go_terms = get_go_annotations(uniprot_id)
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# Summary
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print(f"\n{'='*70}")
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print("WORKFLOW SUMMARY")
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print(f"{'='*70}")
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print(f" Protein: {args.protein}")
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print(f" UniProt ID: {uniprot_id}")
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print(f" Sequence: {'✓' if sequence else '✗'}")
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print(f" BLAST: {'✓' if not args.skip_blast and sequence else '⊘'}")
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print(f" Pathways: {len(pathways)} found")
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print(f" Interactions: {len(interactions)} found")
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print(f" GO annotations: {sum(len(v) for v in go_terms.values())} found")
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print(f"{'='*70}")
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if __name__ == "__main__":
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main()
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Reference in New Issue
Block a user