KOnezumiAID 0.2.1

Project description

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

• bowtie

Install via bioconda

conda install bowtie

or follow the official instruction

Input data set

Locus information

refFlat.text from UCSC

genomic sequence

mm39.fa.gz from UCSC

Download scripts (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