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Splicing Prediction Pipeline

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# SPiP, **S**plicing **P**ipeline **P**rediction
![SPiP logo](https://github.com/raphaelleman/SPiP/blob/master/RefFiles/logoPipeline.gif)

---

SPiP is a randomForest model running a cascade of bioinformatics tools. Briefly, SPiP uses SPiCE tool for the consensus splice sites (donor and acceptor sites), MES for polypyrimidine tract between -13 and -20, BPP for branch point area between -18 and -44, an homemade score to research cryptic/de novo activation and ΔtESRseq for exonic splicing regulatory element until to 120 nt in exon

SPiP is available for Windows OS at https://sourceforge.net/projects/splicing-prediction-pipeline/

**Table**

* [Repository contents](#1)
* [Install SPiP](#2)
    * [Load the transcriptome files](#3)
* [Run SPiP](#4)
    * [SPiP options](#5)
* [Authors](#6)
* [License](#7)

## Repository contents<a id="1"></a>

---

* SPiPv2.1_main.r: the SPiP script
* testCrypt.txt: an example of input data in text format
* testVar.vcf: an example of input data in vcf format
* *RefFiles*: folder where are the reference files used by SPiP

## Install SPiP<a id="2"></a>

---

To get SPiP from this repository, you can enter in the linux consoles:
```shell
git clone https://github.com/raphaelleman/SPiP
cd ./SPiP
```

SPiP needs also to install 2 libraries, from the R console:
```R
install.packages("foreach")
install.packages("doParallel")
install.packages("randomForest")
```

### Load the transcriptome files<a id="3"></a>

you have to download frome sourcforge the RData files containing the transcripts sequences.
**hg19** assembly : [transcriptome_hg19.RData](https://sourceforge.net/projects/splicing-prediction-pipeline/files/transcriptome/transcriptome_hg19.RData/download "tittle")
**hg38** assembly : [transcriptome_hg38.RData](https://sourceforge.net/projects/splicing-prediction-pipeline/files/transcriptome/transcriptome_hg38.RData/download "tittle")

Put these files in `/path/to/SPiP/RefFiles/` or you can define it manually by the option `--transcriptome`.

NB: commands to regenerate these files are available in [getGenomeSequenceFromBSgenome.r](https://github.com/raphaelleman/SPiP/blob/master/RefFiles/getGenomeSequenceFromBSgenome.r "tittle")

## Run SPiP<a id="4"></a>

---

you can get the different argument of SPiP by `Rscript /path/to/SPiPv2.1_main.r --help`

An example of SPiP run with test file [testCrypt.txt](https://github.com/raphaelleman/SPiP/blob/master/testCrypt.txt "tittle"):

```shell
cd /path/to/SPiP/
Rscript ./SPiPv2.1_main.r -I ./testCrypt.txt -O ./outputTest.txt
```

In this example SPiP will generate a text file "outputTest.txt" where the predictions will be save. The scheme of this output is:

### SPiP options <a id="5"></a>

**-I, --input** /path/to/inputFile

+ list of variants file (.txt or .vcf). SPiP supports VCF version 4.1 or later (see example [testVar.vcf](https://github.com/raphaelleman/SPiP/blob/master/testVar.vcf "tittle")). The txt file must be tab-delimated and the column with mutation, in format Transcript:mutation, is indicated by 'varID' column name (see example [testCrypt.txt](https://github.com/raphaelleman/SPiP/blob/master/testCrypt.txt "tittle")).

**-O, --output** /path/to/outputFile

+ Name of ouput file (.txt). Directory to the output file (in text format)

**-g, --GenomeAssenbly** hg19

+ Genome assembly version (hg19 or hg38) [default= hg19]

**-t, --threads** N

+ Number of threads used for the calculation [default= 1]

**-l, --maxLines** N

+ Number of lines read in each time [default= 1000]

**--verbose**

+ Show run process, *i.e.* displays progression bar tool

**--geneList** /path/to/geneList.txt

+ You can process analysis exclusively on a gene list, available only if VCF input

**--transcriptList** /path/to/transcriptList.txt

+ You can process analysis exclusively on a transcript list, available only if VCF input

**--transcriptome** /path/to/transcriptome_hgXX.RData

+ You can define where you have installed the file transcriptome_hgXX.RData if your file is not in /path/to/SPiP/RefFiles/

**--VCF**

+ Get the SPiP output in VCF format (v4.0)

## Authors <a id="6"></a>

* Raphael Leman - [raphaelleman](https://github.com/raphaelleman/ "tittle")
    * You can contact me at: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr

> **Cite as:** Leman, R., Parfait, B., Vidaud, D.,Girodon, E., Pacot, L., Le Gac, G., Ka, C., Ferec, C., Fichou,Y., Quesnelle, C., Aucouturier, C., Muller, E., Vaur, D.,Castera, L., Boulouard, F., Ricou, A., Tubeuf,H., Soukarieh,O., Gaildrat, P., Krieger, S. (2022). SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing. [Human Mutation](https://doi.org/10.1002/humu.24491 "tittle")

## License <a id="7"></a>

This project is licensed under the MIT License - see the [LICENSE](https://github.com/raphaelleman/SPiP/blob/master/LICENSE "tittle") file for details

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