#!/usr/bin/env python3


import re

# Common restriction enzymes and their recognition sites
ENZYMES = {
    "EcoRI": "GAATTC",
    "BamHI": "GGATCC",
    "HindIII": "AAGCTT",
    "XhoI": "CTCGAG",
    "NotI": "GCGGCCGC",
    "SmaI": "CCCGGG",
    "PstI": "CTGCAG",
    "KpnI": "GGTACC",
}


def find_restriction_sites(dna: str, enzymes: dict) -> dict:
    """Find all restriction enzyme cut sites in a DNA sequence."""
    results = {}
    for name, site in enzymes.items():
        positions = [m.start() for m in re.finditer(site, dna, re.IGNORECASE)]
        if positions:
            results[name] = positions
    return results


def print_restriction_map(dna: str, sites: dict) -> None:
    """Print a text-based restriction map."""
    print(f"Restriction map for {len(dna)} bp sequence:")
    print("=" * 60)

    for enzyme, positions in sorted(sites.items(), key=lambda x: x[1][0] if x[1] else 999):
        site = ENZYMES[enzyme]
        for pos in positions:
            print(f"  {enzyme:8s} ({site}) at position {pos + 1}")
            # Show context
            context_start = max(0, pos - 5)
            context_end = min(len(dna), pos + len(site) + 5)
            context = dna[context_start:context_end]
            marker = " " * (pos - context_start) + "^" * len(site)
            print(f"           ...{context}...")
            print(f"            {marker}")


# --- Main program ---
# A sample plasmid sequence (pUC19 MCS region with inserts)
dna = (
    "GAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTT"
    "GGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCA"
    "CACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCT"
    "AACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTG"
    "CCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGC"
    "GAATTCCCT"
)

print(f"DNA sequence: {len(dna)} bp\n")
print(f"Sequence: {dna[:60]}...\n")

# Find all restriction sites
sites = find_restriction_sites(dna, ENZYMES)

# Print the map
print_restriction_map(dna, sites)

# Summary
print(f"\nSummary:")
print(f"  Total enzymes tested: {len(ENZYMES)}")
print(f"  Enzymes with sites: {len(sites)}")
print(f"  Total cut sites: {sum(len(p) for p in sites.values())}")

# Which enzymes cut once? (useful for cloning)
print(f"\nSingle cutters (useful for cloning):")
for enzyme, positions in sites.items():
    if len(positions) == 1:
        print(f"  {enzyme}: position {positions[0] + 1}")

#!/usr/bin/env python3


import os
import re

try:
    from openai import OpenAI
    client = OpenAI(api_key=os.environ.get("OPENAI_API_KEY", ""), base_url=os.environ.get("OPENAI_BASE_URL", "https://openrouter.ai/api/v1"))
    AI_AVAILABLE = True
except ImportError:
    AI_AVAILABLE = False
    print("Note: Install openai package for AI features\n")

def ask_ai(prompt: str) -> str:
    if not AI_AVAILABLE:
        return "(AI not available)"
    return client.chat.completions.create(model=os.environ.get("OPENAI_MODEL", "google/gemini-2.5-flash"), messages=[{"role": "user", "content": prompt}], temperature=0.3).choices[0].message.content

ENZYMES = {"EcoRI": "GAATTC", "BamHI": "GGATCC", "HindIII": "AAGCTT", "XhoI": "CTCGAG", "PstI": "CTGCAG", "KpnI": "GGTACC"}

def find_sites(dna, enzymes):
    results = {}
    for name, site in enzymes.items():
        pos = [m.start() for m in re.finditer(site, dna, re.IGNORECASE)]
        if pos:
            results[name] = pos
    return results

dna = "GAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCGAATTCCCT"

sites = find_sites(dna, ENZYMES)
print(f"Sequence ({len(dna)} bp):")
for enzyme, positions in sites.items():
    print(f"  {enzyme} ({ENZYMES[enzyme]}): position(s) {[p+1 for p in positions]}")

single_cutters = {e: p for e, p in sites.items() if len(p) == 1}
print(f"\nSingle cutters: {list(single_cutters.keys())}")

print("\n--- AI: Help me plan a cloning experiment ---\n")
enzyme_info = "\n".join(f"  {e}: {ENZYMES[e]} at {[p+1 for p in pos]}" for e, pos in sites.items())
result = ask_ai(
    f"I have a {len(dna)} bp plasmid with these restriction sites:\n{enzyme_info}\n\n"
    f"Single cutters: {list(single_cutters.keys())}\n\n"
    "I want to clone a gene into this plasmid. Please explain:\n"
    "1. What are single cutters and why are they important for cloning?\n"
    "2. If my gene has EcoRI sites, which enzyme should I use instead?\n"
    "3. Walk me through the cloning process step by step.\n"
    "4. What is 'ligation' and how does DNA ligase work?\n\n"
    "Explain for a college freshman who has never been in a lab."
)
print(result)

#!/usr/bin/env python3


import sys


def count_bases(dna: str) -> dict:
    """Count each base in a DNA sequence."""
    counts = {}
    for base in dna.upper():
        if base in "ATCG":
            counts[base] = counts.get(base, 0) + 1
    return counts


def main():
    # Check command-line arguments
    if len(sys.argv) < 2:
        # Demo mode if no arguments
        dna = "ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAAC"
        print("(No argument provided -- running with demo sequence)\n")
    else:
        dna = sys.argv[1].upper()

    # Validate
    invalid = [b for b in dna if b not in "ATCG"]
    if invalid:
        print(f"Error: invalid bases found: {set(invalid)}")
        print("DNA sequences should only contain A, T, C, G")
        sys.exit(1)

    print(f"DNA: {dna}")
    print(f"Length: {len(dna)} bases")

    counts = count_bases(dna)
    print("\nBase counts:")
    for base in sorted(counts):
        pct = counts[base] / len(dna) * 100
        print(f"  {base}: {counts[base]} ({pct:.1f}%)")

    gc = (counts.get("G", 0) + counts.get("C", 0)) / len(dna) * 100
    print(f"\nGC content: {gc:.1f}%")


if __name__ == "__main__":
    main()

#!/usr/bin/env python3


import os
import sys

try:
    from openai import OpenAI
    client = OpenAI(api_key=os.environ.get("OPENAI_API_KEY", ""), base_url=os.environ.get("OPENAI_BASE_URL", "https://openrouter.ai/api/v1"))
    AI_AVAILABLE = True
except ImportError:
    AI_AVAILABLE = False

def ask_ai(prompt: str) -> str:
    if not AI_AVAILABLE:
        return "(AI not available)"
    return client.chat.completions.create(model=os.environ.get("OPENAI_MODEL", "google/gemini-2.5-flash"), messages=[{"role": "user", "content": prompt}], temperature=0.3).choices[0].message.content

def main():
    if len(sys.argv) < 2:
        # Demo mode if no arguments
        dna = "ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAAC"
        print("(No argument provided -- running with demo sequence)\n")
    else:
        dna = sys.argv[1].upper()
    invalid = [b for b in dna if b not in "ATCG"]
    if invalid:
        print(f"Error: invalid bases: {set(invalid)}")
        sys.exit(1)

    counts = {b: dna.count(b) for b in "ATCG"}
    gc = (counts["G"] + counts["C"]) / len(dna) * 100

    print(f"DNA: {dna}")
    print(f"Length: {len(dna)}, GC: {gc:.1f}%")

    print("\n--- AI: Sequence validation ---\n")
    result = ask_ai(
        f"Validate this DNA sequence: {dna}\n"
        f"Length: {len(dna)} bp, GC content: {gc:.1f}%\n\n"
        "1. Is this GC content typical of any organism?\n"
        "2. Does it contain any known motifs (start codon, restriction sites)?\n"
        "3. Could this be a coding sequence? Why or why not?\n"
        "4. Suggest 2 experiments to characterize this sequence.\n\n"
        "Be brief and specific."
    )
    print(result)

if __name__ == "__main__":
    main()

#!/usr/bin/env python3


# EXERCISE: This code has 3 bugs. Find and fix them.
# Run it first to see the errors, then fix each one.

# Bug 1: Wrong variable name
dna = "CGACGTCTTCTAAGGCGA"
print(f"DNA: {dna}")

# Bug 2: Off-by-one error in loop
print("\nBases at even positions:")
for i in range(0, len(dna), 2):
    print(f"  Position {i}: {dna[i]}")

# Bug 3: Wrong comparison operator
complement = {"A": "T", "T": "A", "G": "C", "C": "G"}
comp_dna = ""
for base in dna:
    if base in complement:
        comp_dna += complement[base]
    else:
        comp_dna += "N"

print(f"\nComplement: {comp_dna}")
print(f"Reverse complement: {comp_dna[::-1]}")

# SOLUTION (uncomment to verify):
# The bugs are:
# 1. If you used 'DNA' instead of 'dna', Python is case-sensitive
# 2. range(0, len(dna), 2) skips odd positions -- try range(len(dna))
# 3. Using '=' instead of '==' in comparisons (though this example uses 'in')

#!/usr/bin/env python3


import os

try:
    from openai import OpenAI
    client = OpenAI(api_key=os.environ.get("OPENAI_API_KEY", ""), base_url=os.environ.get("OPENAI_BASE_URL", "https://openrouter.ai/api/v1"))
    AI_AVAILABLE = True
except ImportError:
    AI_AVAILABLE = False
    print("Note: Install openai package for AI features\n")

def ask_ai(prompt: str) -> str:
    if not AI_AVAILABLE:
        return "(AI not available)"
    return client.chat.completions.create(model=os.environ.get("OPENAI_MODEL", "google/gemini-2.5-flash"), messages=[{"role": "user", "content": prompt}], temperature=0.3).choices[0].message.content

# This code has intentional bugs for the debugging exercise
buggy_code = '''
dna = "CGACGTCTTCTAAGGCGA"
print("DNA: " + DNA)  # Bug 1: wrong case

complement = {"A": "T", "T": "A", "G": "C", "C": "G"}
comp_dna = ""
for base in dna:
    if base = "A":  # Bug 2: assignment instead of comparison
        comp_dna += complement[base]
    else
        comp_dna += "N"  # Bug 3: missing colon

print("Complement: " + comp_dna)
'''

print("=== BUGGY CODE ===")
print(buggy_code)

print("--- AI: Help me debug this code ---\n")
result = ask_ai(
    f"I'm a student learning Python for bioinformatics. "
    f"This code is supposed to find the complement of a DNA sequence, "
    f"but it has bugs:\n\n{buggy_code}\n\n"
    "Please:\n"
    "1. Identify each bug and explain WHY it's wrong\n"
    "2. Show the corrected code\n"
    "3. Explain the Python rule that each bug violates\n"
    "4. Give me a tip to avoid each type of bug in the future\n\n"
    "Be encouraging -- I'm still learning!"
)
print(result)