Metadata-Version: 2.1
Name: KOnezumiAID
Version: 0.1.2
Summary: Project description
License: MIT
Author: Taki Taito
Author-email: s2110307@u.tsukuba.ac.jp
Requires-Python: >=3.9,<4.0
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: numpy (==1.26.0)
Requires-Dist: pandas (==2.2.2)
Requires-Dist: primer3-py (>=2.0.1,<3.0.0)
Description-Content-Type: text/markdown

# KOnezumi-AID
`KOnezumi-AID` is the command-line tool to automate the gRNA design for multiplex KO mouse using Target-AID

## Installation
### Prerequisits
- Python 3.9 or later
- Unix-like environment (Linux, macOS, WSL, etc.)

### Required Packages
- bedtools

Install via bioconda

`conda install -c conda-forge -c bioconda bedtools`

Install bedtools according to the [official instruction](https://bedtools.readthedocs.io/en/latest/content/installation.html)

- bowtie

Install via bioconda

`conda install bowtie`

or follow the [official instruction](https://bowtie-bio.sourceforge.net/manual.shtml#:~:text=is%20future%20work.-,Obtaining%20Bowtie,-You%20may%20download)

### Input data set
#### Locus information
`refFlat.text` from [UCSC](
https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/
)

#### genomic sequence
`mm39.fa.gz` from [UCSC](
https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/
)

#### Download scripts (bash)

```bash
mkdir -p data
wget -O - https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/refFlat.txt.gz |
    gzip -dc > data/refFlat.txt
wget -O - https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz |
    gzip -dc > data/mm39.fa
```

### Installation🔨
#### Follow these steps to get started with KOnezumiAID from PyPI:

`pip install KOnezumiAID`

## Usage
### Create data set for KOnezumi-AID

`konezumiaid-createdata <your refFlat.txt Path> <your mm39.fa Path>`
### Examples
`konezumiaid-createdata data/refFlat.txt data/mm39.fa`

### Search candidate by gene symbol or transcript name
KOnezumi-AID accepts a gene symbol or a transcript name.

If search by a transcript name, you gan get more information about gRNA.

`konezumiaid <gene symbol or transcript name>`

### Examples
- Search candidate by the gene symbol
```
$konezumiaid Rp1
PTC gRNA
                       seq
0  ACAGGTTATGCAGTGTCCTGTGG
1  ACGACACAGCATCACCAGGCTGG
2  GCCAGGGCCGAGGGCGCCTGCGG
3  ACAGTTTGGCGGCGTTCGGGTGG
4  CCAGGGCCGAGGGCGCCTGCGGG
Acceptor gRNA
No Acceptor gRNA found.
Donor gRNA
No Donor gRNA found.
```

- Search candidate by the transcript name

```
$ konezumiaid NM_001370921
PTC gRNA
                        seq  in_start_150bp  in_50bp_from_LEJ
0   ACAGTTTGGCGGCGTTCGGGTGG            True             False
1   ACGACACAGCATCACCAGGCTGG           False             False
2   ACAGGTTATGCAGTGTCCTGTGG           False             False
3   ACAACCTGTCCTTCCAGGTAAGG           False             False
4   ACCAATCAGAACAATCCCACTGG           False             False
5   ACGAATGTATCTGAGGATTAAGG           False             False
6   TCAGGCCAATGTCACATTGTGGG           False             False
7   CTCAGGCCAATGTCACATTGTGG           False             False
8   CCAGGGCCGAGGGCGCCTGCGGG           False             False
9   GCCAGGGCCGAGGGCGCCTGCGG           False             False
10  TCCAGTGGGATTGTTCTGATTGG           False             False
11  CCAGTACTGGGATTTGTCACTGG           False             False
Acceptor gRNA
                       seq  exon_index
0  ACCTGGGATTGAAAGGAACAAGG          20
1  TCTGTTGGAGAAAAGCCCCATGG          22
2  ACCTGAAGAAAATGGAAAACAGG          23
Donor gRNA
                       seq  exon_index
0  TACCTTGCCCAAGTCCATCATGG           8
1  TTACCTCTCACAGGTGAAGATGG          22
```

