Metadata-Version: 2.4
Name: celljanus
Version: 0.1.6
Summary: CellJanus: Dual-Perspective Deconvolution of Host and Microbial Transcriptomes from FASTQ Data with scRNA-seq Support
Author: Zhaoqing Wang
License: MIT
Project-URL: Homepage, https://github.com/zhaoqing-wang/CellJanus
Project-URL: Repository, https://github.com/zhaoqing-wang/CellJanus
Project-URL: Changelog, https://github.com/zhaoqing-wang/CellJanus/blob/main/CHANGELOG.md
Project-URL: Bug Tracker, https://github.com/zhaoqing-wang/CellJanus/issues
Keywords: bioinformatics,metagenomics,single-cell,spatial-transcriptomics,microbiome,host-microbe,deconvolution,docker
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: click>=8.1
Requires-Dist: rich>=13.0
Requires-Dist: pandas>=2.0
Requires-Dist: numpy>=1.24
Requires-Dist: matplotlib>=3.7
Requires-Dist: seaborn>=0.12
Requires-Dist: biopython>=1.81
Requires-Dist: requests>=2.31
Requires-Dist: tqdm>=4.65
Requires-Dist: psutil>=5.9
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: pytest-cov>=4.0; extra == "dev"
Requires-Dist: black>=23.0; extra == "dev"
Requires-Dist: ruff>=0.1; extra == "dev"
Dynamic: license-file

CellJanus
      
Dual-Perspective Deconvolution of Host and Microbial Transcriptomes from FASTQ Data

           CellJanus Logo

## Features

- **Dual-mode analysis**: Bulk RNA-seq and scRNA-seq pipelines
- **Per-cell tracking**: Cell barcode (CB) and UMI extraction for 10x Genomics, Parse Biosciences
- **Automated pipeline**: QC → Host alignment → Microbial classification → Visualization
- **Comprehensive exports**: 6 CSV formats, 8+ publication-ready plots (PNG/PDF)
- **Large dataset support**: Optimized for 10,000+ cells with smart sampling
- **WSL2 optimized**: Cross-filesystem detection and performance warnings

---

## Pipeline Overview

**Bulk RNA-seq:**
```
FASTQ ─→ fastp (QC) ─→ Bowtie2 (host) ─→ unmapped reads ─→ Kraken2+Bracken ─→ plots + CSV
```

**scRNA-seq:**
```
10x FASTQ ─→ Extract CB+UMI ─→ Kraken2 ─→ Per-cell abundance ─→ Cell×Species matrix
```

---

## Contents

1. [Installation](#installation)
2. [Bulk RNA-seq Mode](#bulk-rna-seq-mode)
3. [scRNA-seq Mode](#scrna-seq-mode)
4. [CLI Reference](#cli-reference)
5. [Python API](#python-api)
6. [Output Structure](#output-structure)
7. [Advanced](#advanced)

---

## Installation

### One-Click Setup (Recommended)

Creates a complete environment with CellJanus **and all external tools** (fastp, Bowtie2, samtools, Kraken2, Bracken):

```bash
# Option 1: From GitHub (recommended)
conda env create -f https://raw.githubusercontent.com/zhaoqing-wang/CellJanus/main/environment.yml
conda activate celljanus
celljanus check   # All tools should show ✔ Found

# Option 2: Clone and install
git clone https://github.com/zhaoqing-wang/CellJanus.git
cd CellJanus
conda env create -f environment.yml
conda activate celljanus
celljanus check
```

> **Requirements**: [Conda](https://docs.conda.io/en/latest/miniconda.html) or [Mamba](https://mamba.readthedocs.io/). Works on **Linux / macOS / WSL2**.

Alternative methods

**pip only** (requires external tools already on PATH):
```bash
pip install celljanus
```

**Development install:**
```bash
git clone https://github.com/zhaoqing-wang/CellJanus.git
cd CellJanus && pip install -e ".[dev]"
```

**Docker:**
```bash
docker build -t celljanus . && docker run --rm celljanus celljanus check
```

**WSL2 (Ubuntu) with APT:**
```bash
# Install external tools
sudo apt-get update
sudo apt-get install -y fastp bowtie2 samtools kraken2

# Install Bracken from source
git clone https://github.com/jenniferlu717/Bracken.git /opt/Bracken
cd /opt/Bracken && bash install_bracken.sh
sudo ln -sf /opt/Bracken/bracken /usr/local/bin/bracken

# Install CellJanus
pip install celljanus --break-system-packages
celljanus check
```


---

## Bulk RNA-seq Mode

Full pipeline: QC → Host alignment → Microbial classification → Visualization.

### Quick Test

Run immediately with built-in test data — **no downloads required**:

```bash
celljanus run \
    --read1 testdata/reads_R1.fastq.gz \
    --read2 testdata/reads_R2.fastq.gz \
    --host-index testdata/refs/host_genome/host \
    --kraken2-db testdata/refs/kraken2_testdb \
    --output-dir test_results/bulk
```

**Test Results** (~4 seconds):

| Metric | Value |
|--------|-------|
| Input reads | 1,000 |
| QC-passed | 950 (95%) |
| Species detected | 5 |

| Species | Reads | Fraction |
|---------|------:|----------|
| *Staphylococcus aureus* | 109 | 37.1% |
| *Escherichia coli* | 79 | 26.9% |
| *Klebsiella pneumoniae* | 56 | 19.0% |
| *Acetitomaculum* | 31 | 10.5% |
| *Longispora* | 19 | 6.5% |

**Example Output:**

| Pipeline Dashboard |
|:--:|
| ![Dashboard](docs/pipeline_dashboard.png) |

| Abundance Bar | Abundance Pie | Abundance Heatmap |
|:--:|:--:|:--:|
| ![Bar](docs/abundance_bar.png) | ![Pie](docs/abundance_pie.png) | ![Heatmap](docs/abundance_heatmap.png) |

### Real Data

```bash
# 1. Download references (~13 GB total)
celljanus download hg38 -o ./refs           # Human genome (~5 GB)
celljanus download kraken2 -o ./refs        # Kraken2 DB (~8 GB)

# 2. Run pipeline
celljanus run \
    -1 sample_R1.fastq.gz -2 sample_R2.fastq.gz \
    -x ./refs/bowtie2_index/GRCh38_noalt_as \
    -d ./refs/standard_8 \
    -o ./results --threads 8
```

---

## scRNA-seq Mode

Per-cell microbial abundance tracking with barcode extraction.

### Quick Test

Run immediately with built-in test data — **no downloads required**:

```bash
celljanus scrnaseq \
    --read1 testdata/scrnaseq/scrna_R1.fastq.gz \
    --read2 testdata/scrnaseq/scrna_R2.fastq.gz \
    --kraken2-db testdata/refs/kraken2_testdb \
    --output-dir test_results/scrnaseq \
    --barcode-mode 10x \
    --min-reads 1
```

**Test Results** (~2 seconds):

| Metric | Value |
|--------|-------|
| Input reads | 15,000 |
| Cells processed | 300 |
| Species detected | 7 |
| Microbial reads | 2,395 |
| Mean reads/cell | 8.0 |

| Species | Reads | Cells | Prevalence |
|---------|------:|------:|-----------:|
| *Escherichia coli* | 460 | 235 | 78.3% |
| *Prevotella* | 426 | 234 | 78.0% |
| *Staphylococcus aureus* | 418 | 218 | 72.7% |
| *Klebsiella pneumoniae* | 405 | 225 | 75.0% |
| *Acetitomaculum* | 311 | 195 | 65.0% |
| *Longispora* | 228 | 134 | 44.7% |
| *Mobiluncus* | 147 | 108 | 36.0% |

**Example Output:**

| scRNA-seq Dashboard |
|:--:|
| ![scRNA-seq Dashboard](docs/scrnaseq_dashboard.png) |

| Species Abundance Pie | Microbial Summary |
|:--:|:--:|
| ![Abundance Pie](docs/scrnaseq_abundance_pie.png) | ![Summary](docs/cell_microbe_summary.png) |

### Real Data

```bash
celljanus scrnaseq \
    --read1 sample_R1.fastq.gz --read2 sample_R2.fastq.gz \
    --kraken2-db ./refs/standard_8 \
    --output-dir scrna_results \
    --barcode-mode 10x --threads 8
```

### Supported Platforms

| Platform | Mode | Barcode Location |
|----------|------|------------------|
| 10x Genomics | `10x` | Header: `CB:Z:BARCODE UB:Z:UMI` |
| Parse Biosciences | `parse` | Read name (colon-separated) |
| Custom | `auto` | Auto-detect |

### Output Files

| File | Description |
|------|-------------|
| `cell_species_counts.csv` | Raw counts (cells × species) |
| `cell_species_normalized.csv` | CPM-normalized for Seurat/Scanpy |
| `cell_species_long.csv` | Tidy format for ggplot2/seaborn |
| `species_summary.csv` | Per-species statistics |
| `cell_summary.csv` | Per-cell diversity metrics |

---

## CLI Reference

| Command | Description |
|---------|-------------|
| `celljanus run` | Full pipeline: QC → Align → Classify → Visualize |
| `celljanus scrnaseq` | scRNA-seq mode with per-cell tracking |
| `celljanus qc` | Quality control (fastp) |
| `celljanus align` | Host alignment (Bowtie2) |
| `celljanus classify` | Taxonomic classification (Kraken2 + Bracken) |
| `celljanus visualize` | Generate abundance plots |
| `celljanus download` | Download reference databases |
| `celljanus check` | Verify tool installation |

### Key Options

| Option | Default | Description |
|--------|---------|-------------|
| `-1, --read1` | *required* | R1 FASTQ file |
| `-2, --read2` | — | R2 FASTQ (paired-end) |
| `-x, --host-index` | *required* | Bowtie2 index prefix |
| `-d, --kraken2-db` | *required* | Kraken2 database path |
| `-o, --output-dir` | `celljanus_output` | Output directory |
| `-t, --threads` | auto | Worker threads |

Run `celljanus <command> --help` for full details.

---

## Python API

### Bulk Pipeline

```python
from pathlib import Path
from celljanus.config import CellJanusConfig
from celljanus.pipeline import run_pipeline

cfg = CellJanusConfig(
    output_dir=Path("./results"),
    host_index=Path("./refs/bowtie2_index/GRCh38_noalt_as"),
    kraken2_db=Path("./refs/standard_8"),
    threads=8,
)

result = run_pipeline(Path("sample_R1.fastq.gz"), read2=Path("sample_R2.fastq.gz"), cfg=cfg)
result.bracken_df           # Species abundance DataFrame
result.qc_report.summary()  # QC statistics
```

### scRNA-seq Pipeline

```python
from celljanus.scrnaseq import BarcodeConfig, run_scrnaseq_classification

result = run_scrnaseq_classification(
    Path("sample_R1.fastq.gz"),
    Path("./refs/standard_8"),
    Path("./scrna_results"),
    read2=Path("sample_R2.fastq.gz"),
    barcode_cfg=BarcodeConfig(mode="10x"),
)

# Access data
abundance = result["abundance"]
abundance.to_matrix()             # Raw counts
abundance.to_normalized_matrix()  # CPM-normalized
abundance.to_species_summary()    # Species statistics
abundance.to_cell_summary()       # Cell diversity metrics
```

---

## Output Structure

### Bulk RNA-seq

```
test_results/bulk/
├── 01_qc/                        # Quality control (fastp)
│   ├── *_qc.fastq.gz            # Trimmed reads
│   ├── *_fastp.json              # QC metrics (machine-readable)
│   └── *_fastp.html              # QC report (interactive)
├── 02_alignment/                 # Host alignment (Bowtie2)
│   ├── host_aligned.sorted.bam   # Full alignment
│   ├── host_mapped.sorted.bam    # Host-only reads
│   ├── unmapped_R{1,2}.fastq.gz  # Non-host → classification
│   └── host_align_stats.txt      # Alignment statistics
├── 04_classification/            # Microbial classification
│   ├── kraken2_report.txt        # Taxonomic report
│   ├── kraken2_output.txt        # Per-read assignments
│   └── bracken_S.txt             # Species-level abundance
├── 05_visualisation/plots/       # Figures (4 PNG + 4 PDF)
│   ├── abundance_bar.*           # Top species bar chart
│   ├── abundance_pie.*           # Donut chart
│   ├── abundance_heatmap.*       # Heatmap (log₁₀)
│   └── pipeline_dashboard.*      # Summary dashboard
├── 06_tables/                    # Machine-readable results
│   ├── species_abundance.csv     # Species × reads × fraction
│   ├── pipeline_summary.csv      # Per-step metrics
│   └── output_manifest.csv       # File inventory
└── celljanus.log                 # Pipeline log
```

### scRNA-seq

```
test_results/scrnaseq/
├── classification/               # Kraken2 output
│   ├── kraken2_report.txt        # Taxonomic report
│   └── kraken2_output.txt        # Per-read assignments
├── tables/                       # 6 CSV exports
│   ├── cell_species_counts.csv   # Raw counts (cells × species)
│   ├── cell_species_normalized.csv # CPM-normalized (Seurat/Scanpy)
│   ├── cell_species_long.csv     # Tidy format (ggplot2/seaborn)
│   ├── species_summary.csv       # Per-species statistics
│   ├── cell_summary.csv          # Per-cell diversity metrics
│   └── pipeline_summary.csv      # Pipeline metrics
├── visualisation/plots/          # Figures (3 PNG + 3 PDF)
│   ├── scrnaseq_dashboard.*      # Summary dashboard
│   ├── scrnaseq_abundance_pie.*  # Community composition donut
│   └── cell_microbe_summary.*    # Distribution panels (3-panel)
└── celljanus.log                 # Pipeline log
```

---

## Advanced

### WSL2 Optimization

For best performance on WSL2, store data on the Linux filesystem:

```bash
# Copy to Linux filesystem (10-50× faster I/O)
mkdir -p ~/celljanus_work
cp /mnt/c/Data/sample*.fastq.gz ~/celljanus_work/

# Run from Linux path
celljanus run -1 ~/celljanus_work/sample_R1.fastq.gz ...
```

CellJanus auto-detects WSL2 and warns about slow cross-filesystem paths.

---

## Citation

```
Wang Z (2026). CellJanus: Dual-Perspective Deconvolution of Host and Microbial Transcriptomes from FASTQ Data.
https://github.com/zhaoqing-wang/CellJanus
```

## License

[MIT](LICENSE)

## Contact

**Author:** Zhaoqing Wang ([ORCID](https://orcid.org/0000-0001-8348-7245)) | **Email:** <zhaoqingwang@mail.sdu.edu.cn> | **Issues:** [CellJanus Issues](https://github.com/zhaoqing-wang/CellJanus/issues)
