semvec/pypi-packages huggingface dataset:
decon2vcf 1.0.1
Convert Decon Output to VCF format.

# DeconToVCF

## Introduction

This is a tool to convert multiple DeCon .txt [1] file outputs generated in pipelines into a single genomic VCF format file that can then be used for annotation software and further analysis tools.

## Download the directory:
```
git clone git@github.com:AWGL/DeconToVCF.git
```

## Requirements

The python script needs to be run with arguments

* -d = path to decon output directory. The directory should be the folder containing all of the decon outputs "raw_data".
* -p = path to ped file.
* -o = path and filename of choice for the output. The programme will not create directories that do not already exist.


## To run the programme

* create environment from .yaml file and activate
```
pip install decon2vcf
```

* run programme with arguments
```
python DeconToVCF -d <path-to-decon-output-directory> -p <path-to-ped-file> -o <path/filename-for-output-file>
```
  eg:
```
python DeconToVCF -d /data/runid/post-processing/results/cnv_svs/raw_data/ -p post-processing/results/ped/file.ped -o post-processing/results/DeconToVCF_output.vcf
```

## References

[1] https://www.imm.ox.ac.uk/research/research-groups/lunter-group/lunter-group/decon-detection-of-exon-copy-number
flow-utils 0.0.1
deeplearning utils based on OneFlow

# oneflow-utils
Deeplearning Utils base on OneFlow

## Pre-requisites
```bash
$ pip install oneflow-utils==0.0.1
```

## Contents
### 1. Cosine / Linear LR Schedule with Warmup
- Source Code: [Cosine LR](https://github.com/rentainhe/oneflow-utils/blob/main/schedulers/cosine_lr.py) / [Linear LR](https://github.com/rentainhe/oneflow-utils/blob/main/schedulers/linear_lr.py)

- Usage
```python
from oneflow-utils import WarmupLinearSchedule, WarmupCosineSchedule
```
oneflow-utils 0.0.1
deeplearning utils based on OneFlow

# oneflow-utils
Useful Utils in OneFlow

## Pre-requisites
```bash
$ pip install oneflow-utils==0.0.1
```

## Contents
### 1. Cosine / Linear LR Schedule with Warmup
- Source Code: [Cosine LR]() / [Linear LR]()

- Usage
```python
from oneflow-utils import WarmupLinearSchedule, WarmupCosineSchedule
```