file_generator.py

import os

# Base directory - CHANGE THIS TO YOUR PATH
base_dir = r"C:\Users\HOME\.vscode\Mini-Bio-Python-Projects"

# Define all phases with their projects
phases = {
    "phase1_foundation": [
        "dna_base_counter",
        "gc_content_calc",
        "dna_melting_temp",
        "protein_charge_calc",
        "codon_table_lookup",
        "restriction_site_finder",
        "dna_complement_generator",
        "reverse_transcription",
        "primer_dimer_detector",
        "reading_frame_translator",
        "snp_classifier",
        "dna_motif_scorer",
        "cell_division_timer",
        "ph_buffer_calc",
        "genetic_code_explorer"
    ],
    "phase2_control": [
        "sequence_alignment_scorer",
        "phylogenetic_distance_matrix",
        "orf_finder",
        "dna_shuffle_simulator",
        "codon_usage_bias",
        "protein_property_profiler",
        "genetic_drift_simulator",
        "hardy_weinberg_tester",
        "enzyme_kinetics_calc",
        "dna_barcode_validator",
        "gene_expression_simulator",
        "pedigree_analysis",
        "blast_hit_parser",
        "vcf_info_extractor",
        "fasta_header_parser"
    ],
    "phase3_data_structures": [
        "genome_feature_coords",
        "protein_domain_parser",
        "genetic_cross_simulator",
        "restriction_map_generator",
        "dna_assembly_simulator",
        "primer_design_assistant",
        "sanger_trace_simulator",
        "allele_frequency_tracker",
        "go_term_enrichment",
        "msa_viewer",
        "newick_tree_parser",
        "protein_interaction_network",
        "codon_pair_bias",
        "genome_browser_mini_api",
        "metabolic_pathway_sim"
    ],
    "phase4_comprehensions": [
        "fastq_quality_trimmer",
        "gff3_extractor",
        "vcf_filter_tool",
        "bedtools_intersect",
        "sam_flag_decoder",
        "bam_depth_calc",
        "fai_builder",
        "multi_fasta_splitter",
        "expression_matrix_norm",
        "de_simulator",
        "gwas_stats_cleaner",
        "clinvar_annotator",
        "ensembl_api_fetcher",
        "pubmed_abstract_miner",
        "sequence_logo_generator"
    ],
    "phase5_numpy": [
        "dna_signal_processor",
        "protein_distance_matrix",
        "ramachandran_plot",
        "electrostatic_surface",
        "md_trajectory_analyzer",
        "hmm_cpg_islands",
        "gmm_cell_clustering",
        "diversity_index_calc",
        "phylip_distance_tree",
        "qtl_mapping_sim",
        "neural_spike_analyzer",
        "calcium_imaging_extractor",
        "dna_melting_curve",
        "binding_kinetics_fitter",
        "cryoem_resolution_est"
    ],
    "phase6_pandas": [
        "tcga_data_harmonizer",
        "drug_response_analyzer",
        "sc_metadata_aggregator",
        "maxquant_parser",
        "metabolomics_peak_analyzer",
        "lab_report_generator",
        "epidemiological_tracer",
        "clinical_trial_validator",
        "biobank_tracker",
        "multi_omics_integration"
    ],
    "phase7_matplotlib": [
        "genome_coverage_plotter",
        "manhattan_plot_gen",
        "volcano_plot_annotated",
        "oncoprint_generator",
        "phylo_tree_heatmap",
        "flow_cytometry_gating",
        "protein_structure_cartoon"
    ],
    "phase8_ml": [
        "dna_kmer_classifier",
        "protein_ss_predictor",
        "cancer_classifier",
        "drug_property_predictor",
        "survival_risk_stratifier",
        "variant_pathogenicity",
        "sc_cell_type_classifier",
        "multimodal_outcome_predictor"
    ]
}

# Files to create in each project folder
project_files = [
    "main.py",
    "README.md",
    "requirements.txt",
    "data/.gitkeep",
    "output/.gitkeep",
    "tests/.gitkeep"
]

# Root level files
root_files = [
    "README.md",
    "roadmap.md",
    ".gitignore",
    "setup.py",
    "pyproject.toml"
]

# Create base directory
os.makedirs(base_dir, exist_ok=True)

# Create all directories and files
created_count = 0

for phase_name, projects in phases.items():
    phase_path = os.path.join(base_dir, phase_name)
    os.makedirs(phase_path, exist_ok=True)
    
    for project in projects:
        project_path = os.path.join(phase_path, project)
        
        # Create project files
        for file_path in project_files:
            full_path = os.path.join(project_path, file_path)
            dir_name = os.path.dirname(full_path)
            
            # Create subdirectory if needed
            if dir_name and not os.path.exists(dir_name):
                os.makedirs(dir_name, exist_ok=True)
            
            # Create file with UTF-8 encoding
            if not file_path.endswith('.gitkeep'):
                with open(full_path, 'w', encoding='utf-8') as f:
                    if file_path == "README.md":
                        f.write(f"# {project.replace('_', ' ').title()}\n\nProject description and documentation.\n")
                    elif file_path == "requirements.txt":
                        f.write("# Add project-specific dependencies here\n")
                    elif file_path == "main.py":
                        f.write(f'"""\n{project.replace("_", " ").title()}\n\nBiology-themed Python project.\n"""\n\ndef main():\n    pass\n\nif __name__ == "__main__":\n    main()\n')
            else:
                # Create .gitkeep file
                with open(full_path, 'w', encoding='utf-8') as f:
                    pass
            
            created_count += 1

# Create root level files with UTF-8 encoding
for root_file in root_files:
    full_path = os.path.join(base_dir, root_file)
    with open(full_path, 'w', encoding='utf-8') as f:
        if root_file == "README.md":
            f.write("""# Bio-AI 100 Python Projects

Complete biology-themed Python curriculum from beginner to pro.

## Structure

- **Phase 1**: Foundation (Projects 1-15)
- **Phase 2**: Control & Structure (Projects 16-30)
- **Phase 3**: Data Structures & Functions (Projects 31-45)
- **Phase 4**: Comprehensions & File Handling (Projects 46-60)
- **Phase 5**: NumPy & SciPy (Projects 61-75)
- **Phase 6**: Pandas & Data Analysis (Projects 76-85)
- **Phase 7**: Matplotlib & Seaborn (Projects 86-92)
- **Phase 8**: Scikit-Learn & ML (Projects 93-100)

## Quick Start

```bash
# Navigate to any project
cd phase1_foundation/dna_base_counter

# Install dependencies
pip install -r requirements.txt

# Run the project
python main.py
```
""")
        elif root_file == "roadmap.md":
            f.write("""# Project Roadmap

## Progress Tracker

| Phase | Projects | Status |
|-------|----------|--------|
| Phase 1: Foundation | 1-15 | [ ] Not Started |
| Phase 2: Control | 16-30 | [ ] Not Started |
| Phase 3: Data Structures | 31-45 | [ ] Not Started |
| Phase 4: Comprehensions | 46-60 | [ ] Not Started |
| Phase 5: NumPy | 61-75 | [ ] Not Started |
| Phase 6: Pandas | 76-85 | [ ] Not Started |
| Phase 7: Visualization | 86-92 | [ ] Not Started |
| Phase 8: ML | 93-100 | [ ] Not Started |

## Learning Path

1. Complete each phase in order
2. Build portfolio as you progress
3. Combine projects for capstone work
""")
        elif root_file == ".gitignore":
            f.write("""# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
env/
venv/
.venv/
pip-log.txt

# Data files (keep structure, ignore large files)
*.fasta
*.fastq
*.bam
*.sam
*.vcf
*.gz
*.zip
*.tar

# Output
data/*
!data/.gitkeep
output/*
!output/.gitkeep

# IDE
.vscode/
.idea/
*.swp
*.swo

# OS
.DS_Store
Thumbs.db
""")
        elif root_file == "setup.py":
            f.write("""from setuptools import setup, find_packages

setup(
    name="bio-ai-100-projects",
    version="1.0.0",
    description="Biology-themed Python curriculum",
    packages=find_packages(),
    python_requires=">=3.8",
)""")
        elif root_file == "pyproject.toml":
            f.write("""[build-system]
requires = ["setuptools>=45", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "bio-ai-100-projects"
version = "1.0.0"
description = "Biology-themed Python curriculum from beginner to pro"
requires-python = ">=3.8"
dependencies = [
    "numpy",
    "pandas",
    "matplotlib",
    "seaborn",
    "scipy",
    "scikit-learn",
    "biopython",
]

[tool.black]
line-length = 88

[tool.pytest.ini_options]
testpaths = ["tests"]""")

print(f"Created {len(phases)} phases with {sum(len(p) for p in phases.values())} projects")
print(f"Total files created: {created_count + len(root_files)}")
print("\nDone! Folder structure created successfully.")