# CellTics

**Repository Path**: handsun1/CellTics

## Basic Information

- **Project Name**: CellTics
- **Description**: 合并vcf邻近位点的工具
来源：https://github.com/MGHComputationalPathology/CellTics
修改了配置文件信息使安装更容易，修改一处bug
- **Primary Language**: Python
- **License**: BSD-3-Clause
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2022-03-08
- **Last Updated**: 2022-03-09

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# CellTics
Center for Integrated Diagnostics at Mass General Hospital NGS tools

## Installation
```
conda create -p /home/work/software/celltics python==3.5
cd /home/work/software/celltics
git clone https://gitee.com/handsun1/CellTics.git
cd CellTics
virtualenv --python=/home/work/software/celltics/bin/python3 venv3
source venv3/bin/activate
pip install -r requirements.txt -i https://pypi.tuna.tsinghua.edu.cn/simple
python3 setup.py install
```

If you receive an error pertaining to lzma.h you may need to disable lzma and try python setup.py install again. (This occurs on MacOS Mojave)
```
export HTSLIB_CONFIGURE_OPTIONS=--disable-lzma
python setup.py install
```

With Mac OS High Sierra there is a new security feature to disable multithreading.  If you see an error such as:

```bash
objc[49174]: +[__NSPlaceholderDate initialize] may have been in progress in another thread when fork() was called.                                                                                          
objc[49174]: +[__NSPlaceholderDate initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set 
a breakpoint on objc_initializeAfterForkError to debug.
```

set the following environment variable:
```bash
export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES

```

## VarGroup
Scans a vcf file and combines multiple nearby SNPs and indels into a single genomic event.

The pickle library DOES NOT work with the cli library which allows calling celltics directly.  When multithreading you must call

```bash
python /path/to/celltics/tools/vargroup.py -i <input> -o <output>
```

VarGrouper runs multithreaded by default.  Use --debug or set threads to 1 (-t 1) to avoid multiprocessing.

### Simplest vargroup command
_This will produce a warning if invoked with the cli library._
```bash
celltics vargroup --input-file sorted_variants.vcf --output-file grouped_variants.vcf --ref-seq hg19.fasta -t 1
```
or (no warning message)
```bash
python celltics/tools/vargroup.py --input-file sorted_variants.vcf --output-file grouped_variants.vcf --ref-seq hg19.fasta -t 1
```

### Run vargroup with bam
```bash
celltics vargroup --input-file sorted_variants.vcf --output-file grouped_variants.vcf --bam-file sorted_alignment.bam --ref-seq hg19.fasta -t
```
or (no warning message)
```bash
python celltics/tools/vargroup.py --input-file sorted_variants.vcf --output-file grouped_variants.vcf --bam-file sorted_alignment.bam --ref-seq hg19.fasta -t 1
```
If a reference sequence is not supplied the UCSC hg19 api is queried ([http://genome.ucsc.edu/](http://genome.ucsc.edu/)).  Variants will be grouped if they are within a certain distance and occur on the same reads.  For more advanced options run ```celltics vargroup --help```.

### Troubleshooting
Errors are not very informative when masked by the python multithreading module.  Run vargroup with --debug and error messages are more informative.

### Algorithm
![VarGrouper](https://gitee.com/handsun1/CellTics/blob/master/celltics/docs/graphics/vargrouper_flow.png)

### Version 2.0
- added multiprocessing
- converted from python 2.7 to python 3

### Contact

* [Allison MacLeay](mailto:allison.macleay@gmail.com)
* [Ryan Schmidt](mailto:RSCHMIDT@BWH.HARVARD.EDU)