semvec/pypi-packages huggingface dataset:
leen 0.0.1
A package to judge whether a EBI code correspond to a sentence

# leen

A package to judge whether a EBI code correspond to a sentence

## Requirements

- torch 8
- Python >= 3.5

## Installation
You can use pip to install our package, similar to other packages

```bash
pip3 install leen
```

```python
import leen.test as le
le.same(EBI-id, sentence) #note that both parameters should be enclosed in quotations when typing pure string
le.description(EBI-id) #also, EBI-id should be quotated
```

## Usage
* description(EBI-id)
	* a fuction getting the description corresponding to idcode
	* input:str EBI-id
	* return:str description

* same(EBI-id, sentence)
	* a function judging whether a EBI-id correspond to a description，return True/False 
    * input:str idcode,str sentence
	* output:bool True/False

## Note
* parameters should be enclosed in quotations when typing pure string
* `torch 8` is Indispensable when using our package

## FAQ
* What is `EBI-id` in the description of `usage` above?
    * It is the accession number of the interaction in the IntAct database.

* How can I contribute to the project?
	* Our project is on "https://gitlab.com/BioAI/leen" ,your contribution is highly appreciated.
baseqRNA 1.5
Pipeline for Processing RNA-Seq datasets
Keywords: sample setuptools development

# DropRNA

## Install baseq_drops
We need python3 and a package called: baseq_drops, which could be installed by:

    pip install baseqdrops

After install, you will have a runnable command `baseq-Drop`

## Config file

The pipeline need the following software or resources:

+ `star`: STAR software, for fast alignment of RNA-Seq data;
+ `samtools`: Sorting bam file;
+ `whitelistDir`: The barcode whitelist files for indrop and 10X should be placed under whitelistDir.
These files can be downloaded from XXX.
+ `cellranger_ref_<genome>`: The key process of read alignment and tagging to genes
 are inspired and borrowed from the open source cellranger pipeline
 (https://github.com/10XGenomics/cellranger).
 The refernces of genome index and transcriptome can be downloaded
 from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest.
In the config file, the directory of cellrange references is named as `cellranger_<genome>`.

While running command, the configures are recorded in the file called `config_drops.ini`:

    [Drops]
    samtools = /path/to/samtools
    star = /path/to/STAR
    whitelistDir = /path/to/whitelist_file_directory
    cellranger_hg38 = /path/to/reference/refdata-cellranger-GRCh38-1.2.0/

## Process Steps
1. `Extract the Cell Barcode` Counting the number of each kinds of barcode; this will genrate a barcode_count.<sample>.csv;
2. `Cell Barcode correction and filtering` Correcting the cell barcode with 1bp mismatch, filtering the barcode with min number of reads;
3. `Split the reads of valid Cell Barcodes` The raw pair-end raw reads are splitted to 16 single end files for multiprocessing according to the 2bp prefix of barcode; For example, we will get: split.<sample>.<AA|AT|AC|AG...|GG>.fq
4. `Star Alignment` Fastq files runs at the same time; The bam file sorted by sequence header is generated;
5. `Reads tagging` Tagging the reads alignment position to the corresponding gene name
6. `Genrating UMI table`

## Run Command

The main config is:

+ `--config`: config file;
+ `--genome/-g`: genome version;
+ `--protocol`: [10X|indrop|dropseq]
+ `--minreads`:  Minimum reads for a barcode
+ `--name/-n` : Sample name
+ `--fq1/-1`: Read 1
+ `--fq2/-2`: Read 2
+ `--top_million_reads`: How many million reads to use, mainly for testing pipeline with fraction of reads (default 1000)
+ `--dir/-d`: output path

If you config the: `cellranger_ref_hg38` you can run the following:

    baseqdrops run_pipe --config ./config_drops.ini -g hg38 -p 10X --minreads 10000 -n 10X_test -1 10x_1.1.fq.gz -2 10x.2.fq.gz -d ./

### For older version 10X results
The cell barcode length is 15 and UMI length is 5.

    baseqdrops run_pipe --config ./config_drops.ini -g hg38 -p 10X --minreads 10000 -n 10X_test -1 10x_1.1.fq.gz -2 10x.2.fq.gz -d ./