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A package for estimating alternative polyadenylation events from scRNA-seq data.

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## SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data

### Installation

#### Method 1
```
conda config --append channels bioconda 
conda config --append channels conda-forge 
conda config --append channels anaconda 
conda create -n scape_env python=3.11
conda activate scape_env

conda install anaconda::numpy
conda install anaconda::scipy
conda install anaconda::pandas
conda install anaconda::matplotlib
conda install anaconda::click
conda install anaconda::tomli-w
conda install anaconda::requests
conda install conda-forge::psutil
conda install conda-forge::tomli-w
conda install bioconda::bedtools
conda install bioconda::pybedtools
conda install bioconda::pysam
conda install bioconda::gffutils

pip install taichi
pip install scape-apa
```

#### Method 2
```
# Mac
conda env create -f mac_environment.yml
conda activate scape_env
```

#### Method 3
```
# Linux
conda env create -f linux_environment.yml
conda activate scape_env
pip install -r linux_requirements.txt
```

#### Method 4
```
# install locally
git clone https://github.com/chengl7-lab/scape.git
cd scape
pip install .
```

### Commands

| Command | Description |
| --- | --- |
| scape gen_utr_annotation | Generate UTR annotation. |
| scape prepare_input | Prepare data per UTR. |
| scape infer_pa | Parameters inference. |
| scape merge_pa | Merge PA within junction per gene or UTR. |
| scape cal_exp_pa_len | Calculate the expected length of PA. |
| scape ex_pa_cnt_mat | Extract read count matrix. |

Get help information of `scape` or `scape commands`.
```
scape --help
scape gen_utr_annotation --help
```

### Usage

#### gen_utr_annotation

| Input Argument |  Type | Required | Default | Description |
| --- | --- |  --- |  --- |  --- | 
| --gff_file           | TEXT | Yes | NA  |  The gff3 or gff3.gz file including annotation of gene body. |
| --output_dir         | TEXT | Yes | NA  | Directory to save dataframe of selected UTR. |
| --res_file_name      | TEXT | Yes | NA  | File Name of dataframe of the UTR annotation. The suffix `.csv` is automatically generated. |
| --gff_merge_strategy | TEXT | No  | merge | Method for processing overlapping regions. It follows `merge_strategy` in package gffutils. |

OUTPUT: An csv file including information of annotated 3UTR which is stored at `{output_dir}/{res_file_name}.csv`.

#### prepare_input

| Input Argument |  Type | Required | Default | Description |
| --- | --- |  --- |  --- |  --- | 
| --utr_file  | TEXT    |Yes | NA |  UTR annotation file (dataframe, resulted from gen_utr_annotation).|
| --cb_file   | TEXT    |Yes | NA | File of tsv.gz including all validated barcodes (by CellRanger). This file has one column of cell barcode which must be consistent with value of CB tag in bam_file file. |
| --bam_file  | TEXT    |Yes | NA | Bam file that is used for searching reads over annotated UTR.|
| --output_dir| TEXT    |Yes | NA | Output directory to save pickle files of selected reads over annotated UTR. |
| --chunksize |INTERGER | No |1000 | Number of UTR regions included in each small pickle file, which contains the preprocessed input file for APA analysis. |

OUTPUT: Pickle files that include tuples (gene info, dataframe of parameter).

#### infer_pa

| Input Argument |  Type | Required | Default | Description |
| --- | --- |  --- |  --- |  --- | 
| --input_pickle_file  | TEXT    |Yes | NA | Input pickle file (result of prepare_input)|
| --output_dir         | TEXT    |Yes | NA | Directory to save output pickle files including PAS information over annotated UTR. |
| --toml_para_file | TEXT | No | None | A TOML file ([example](./tutorial/default_config.toml)) specifies user-defined parameters.  | 
| --pre_para_pkl_file | TEXT | No | None | A pickle file with pre-specified pA sites and utr length, result file of scape analysis. |

OUTPUT: Pickle file including Parameters for each UTR region.

#### merge_pa

| Input Argument |  Type | Required | Default | Description |
| --- | --- |  --- |  --- |  --- | 
| --output_dir  | TEXT       |Yes | NA | Directory which was used in previous steps to save output by `prepare_input` and `infer_pa`.|
| --utr_merge   | BOOLEAN    |No | True | If True, PA sites from the same gene are merge. Otherwise, if False, PA sites from the same UTR are merged. |

OUTPUT: A single pickle file containing all UTRs of all genes is stored in `output_dir/`. Its name is `res.gene.pkl` if `utr_merge=True`, otherwise, its name is `res.utr.pkl`.

#### cal_exp_pa_len

| Input Argument |  Type | Required | Default | Description |
| --- | --- |  --- |  --- |  --- | 
| --output_dir        | TEXT  |Yes | NA | Directory which was used in previous steps to save output by `prepare_input` and `infer_pa`.|
| --cell_cluster_file | TEXT  |No | - | An `csv` file containing two columns in order: cell barcode (CB) and respective group (cell_cluster_file). Its name will be included in the file name of final result. |
| --res_pkl_file      | TEXT  |No | - | Name of res pickle file that contains PASs for calculating expected PA length. Its name will be included in the file name of final result. |

OUTPUT: `exp_pa_len.csv`. It is a dataframe with 2 columns.

#### ex_pa_cnt_mat

| Input Argument |  Type | Required | Default | Description |
| --- | --- |  --- |  --- |  --- | 
| --output_dir        | TEXT  |Yes | NA | Directory which was used in previous steps to save output by `prepare_input` and `infer_pa`.|
| --res_pkl_file      | TEXT  |No | - | Name of res pickle file that contains PASs for calculating expected PA length. Its name will be included in the file name of final result. |

OUTPUT: An tsv.gz file named {res_pkl_file.cnt.tsv.gz} is stored in `output_dir/`.

### Demo & Tutorials

The data used can be downloaded from [examples](examples/).

- [SCAPE toy example](tutorial/SCAPE-toy-example.ipynb)
- [SCAPE example with differential expression analysis](tutorial/SCAPE-example-with-DE.ipynb)
- [Benchmarks](benchmark/benchmark_btw_old_and_new_version_of_SCAPE.ipynb)

### Citation

Cheng G, Le T, Zhou R and Cheng L. SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data [version 1; peer review: awaiting peer review]. Open Res Europe 2024, 4:220 (https://doi.org/10.12688/openreseurope.18673.1)

[comment]: <> (Release commands)
[comment]: <> (python -m build) 
[comment]: <> (python3 -m twine upload --repository scape-apa dist/*)

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