semvec/pypi-packages huggingface dataset:
capcruncher-tools 0.2.4
Extra utilities to enhance CapCruncher
Requires Python: >=3.8

# CapCruncherTools

## Overview

A collection of Rust tools to speed up the python based functionality of the CapCruncher project. Python binding have been generated to allow for easy integration into the existing python code base. 

## Current Tools

### FASTQ deduplication - fastq-deduplicate:

This tool takes paired FASTQ files and removes any duplicate fragments. 

#### Basic Usage:

```bash
capcruncher-tools fastq-deduplicate -1 <input1.fastq> -2 <input2.fastq> -o <output_prefix>
```


### Restriction digestion of FASTA - digest-genome:

This tool takes a FASTA file and a list of restriction enzymes and produces a list of fragments in BED format.

#### Basic Usage:

```bash
capcruncher-tools digest-genome -i <input.fasta> -o <output.bed> -r <recognition site> -p  <number of threads>
```


### Count restriction fragments - count:

This tool counts the number of interactions between a fragment (in silico digested read).

#### Basic Usage:

```bash
capcruncher-tools count <reporters> -f <fragments.bed> -v <viewpoints_path.bed> -o <output.hdf5> -p <number of threads>
```
python-to-mermaid 0.6.0
Generate Mermaid diagrams using Python code
Requires Python: >=3.7

# python-to-mermaid

Generate [Mermaid diagrams](https://mermaid.js.org/) using Python code.

## Installation

### UV

```bash
uv add python-to-mermaid
```

### Pip

```bash
pip install python-to-mermaid
```

## Usage

```python
from python_to_mermaid import MermaidDiagram

diagram = MermaidDiagram()
diagram.add_node("A")
diagram.add_node("B")
diagram.add_edge("A", "B")

mermaid_diagram = str(diagram)
# flowchart TD
#     A
#     B
#     A --> B
```

```mermaid
flowchart TD
    A
    B
    A --> B
```

## Examples

See the [examples](examples) directory for more examples.

- [Node with Text](examples/node_with_text.md)
- [Node Shapes](examples/node_shapes.md)

## Development

```bash
uv sync
```

## Testing

```bash
pytest tests/ -v
```

## Publishing

```bash
./publish.sh
```

```bash
chmod +x publish.sh
```

### Generate Examples

```bash
python examples
```