autocbei可以计算目标cds的潜在CBEI位点，并进行统计和绘图。
autocbei的Python项目详细描述
奥克贝
我们提供了命令行版本，可用于设计大量CDS的胞嘧啶碱基编辑器介导的基因失活。在
我们开发了“autocbei”来自动计算目标cds的潜在CBEI位点，并进行统计和计算。在
1。安装
“autocbei”依赖python3，需要“biopython”和“matplotlib”包。当前版本（1.6.3）支持“conda”和“pip”安装。在
1.1由conda安装（推荐）
Conda（包括Anaconda和Miniconda）是一种流行的软件管理方法。它可以在不影响全局设置的情况下创建和配置虚拟环境。在
首先安装Anaconda或{a2}的相应平台。我们建议安装python3版本。在
然后执行以下命令：
# Creating a virtual environment of python3.7.1. conda create -n runCBEI python=3.7 -y # Activate the environment2. conda activate runCBEI # Install autocbei3. conda install -c atlasbioinfo autocbei -y
1.2 pip安装
如果操作系统中已经包含Python3（Python>；=3.6.0），则可以通过pip自动安装autocbei。在
^{pr2}$使用以下命令确定已安装的Python版本：
python -V
如果您还没有安装python3，建议使用上面的“方法1.1”。在
1.3安装预发布版本（推荐有经验的用户）
如果您想试用autocbei的最新但unrelease version（可能不稳定），请遵循以下命令：
# Download CRISPR-CBEI from Github1. git clone https://github.com/atlasbioinfo/CRISPR-CBEI.git # Install biopython and matplotlib2. conda install -y biopython matplotlib # Run autocbei and show help info3. python run_autocbei.py -h
2使用
2.1演示CD文件
如果“autocbei”安装成功，则示例文件位于[PYTHON_HOME]/site packages/autocbei/Bacillus_枯草芽孢杆菌500.cds.all.fa在
如果与Conda一起安装，应位于：
~/anaconda3/envs/autocbei/lib/python3.7/site-packages/autocbei/Bacillus_subtilis.part500.cds.all.fa
2.2运行
h参数显示帮助信息。在
autocbei -h
usage: autocbei [-h] [-ns] [-o OUTPREFIX] CDS.fasta
Enter fasta file of CDSs, output base editor's potential editing site and
statistics information. The demo CDS Fasta file: "[PATHON_HOME]/site-
packages/autocbei/Bacillus_subtilis.part500.cds.all.fa".
positional arguments:
CDS.fasta CDSs in fasta format.
optional arguments:
-h, --help show this help message and exit
-ns, --nostat Only run CBEI design without statistics and plot.
-o OUTPREFIX, --outprefix OUTPREFIX
Directory prefixes can be customized. Default: "CBEI"
(CBEIRaw, CBEIPlot, CBEIRes).
计算cds潜在的CRISPR库编辑站点信息
autocbei Bacillus_subtilis.part500.cds.all.fa
仅计算而不进行统计和绘图：
autocbei -ns Bacillus_subtilis.part500.cds.all.fa -o Bac
3。基本编辑
autoCBEI包含13个常用的基本编辑器。在
#Set the Base editor parameter# [PAM, spacer length, edit beg, edit end, direction]# Direction refers to spacer at the 5' or 3' end of PAM sequence (5 or 3, respectively).beinfos={"BE":["NGG",20,4,8,5],"YE1-BE3":["NGG",20,5,7,5],"EE-BE3":["NGG",20,5,6,5],"YEE-BE3":["NGG",20,6,6,5],"VQR-BE3":["NGAN",20,4,11,5],"VRER-BE3":["NGCG",20,3,10,5],"SaBE":["NNGRRT",21,3,12,5],"Sa(KKH)-BE3":["NNNRRT",21,3,12,5],"Cas12a–BE":["TTTV",20,10,12,3],"Target-AID":["NGG",20,2,4,5],"Target-AID-NG":["NG",20,2,4,5],"xBE3":["NG",20,4,8,5],"BE-PLUS":["NGG",20,4,14,5]# Or, add your own Base editors# "BE name" :[PAM, SpLength, EditBeg, EditEnd, Direction]}
PAM: PAM sequence.
SpLength: Spacer length.
EditBeg: Edit windows begin.
EditEnd: Edit windows end.
Direction: 5 or 3. Spacer is at the 5 'end or 3' end of the PAM sequence. The example in the figure is the 5.
输出4
4.1输出消息
简单运行的输出消息
autocbei Bacillus_subtilis.part500.cds.all.fa
应该是：
Input file: Bacillus_subtilis.part500.cds.all.fa
Output directory: CBEIRaw
Base editors:
BE PAM Spacer EditBegin EditEnd Direction
BE NGG 20 4 8 5
YE1-BE3 NGG 20 5 7 5
EE-BE3 NGG 20 5 6 5
YEE-BE3 NGG 20 6 6 5
VQR-BE3 NGAN 20 4 11 5
VRER-BE3 NGCG 20 3 10 5
SaBE NNGRRT 21 3 12 5
Sa(KKH)-BE3 NNNRRT 21 3 12 5
Cas12a–BE TTTV 20 10 12 3
Target-AID NGG 20 2 4 5
Target-AID-NG NG 20 2 4 5
xBE3 NG 20 4 8 5
BE-PLUS NGG 20 4 14 5
Start calculating: BE
CBEI calculation of base editor "BE" , done!
Start calculating: YE1-BE3
CBEI calculation of base editor "YE1-BE3" , done!
Start calculating: EE-BE3
CBEI calculation of base editor "EE-BE3" , done!
Start calculating: YEE-BE3
CBEI calculation of base editor "YEE-BE3" , done!
Start calculating: VQR-BE3
CBEI calculation of base editor "VQR-BE3" , done!
Start calculating: VRER-BE3
CBEI calculation of base editor "VRER-BE3" , done!
Start calculating: SaBE
CBEI calculation of base editor "SaBE" , done!
Start calculating: Sa(KKH)-BE3
CBEI calculation of base editor "Sa(KKH)-BE3" , done!
Start calculating: Cas12a–BE
CBEI calculation of base editor "Cas12a–BE" , done!
Start calculating: Target-AID
CBEI calculation of base editor "Target-AID" , done!
Start calculating: Target-AID-NG
CBEI calculation of base editor "Target-AID-NG" , done!
Start calculating: xBE3
CBEI calculation of base editor "xBE3" , done!
Start calculating: BE-PLUS
CBEI calculation of base editor "BE-PLUS" , done!
Calculate complete!
Begin statistics...
The statistics directory: CBEIStat
The plot directory: CBEIPlot
####################
Pie charts for different BEs have been generated.
Path:
CBEIPlot/[BE names]_Bacillus_subtilis.statPie.png
Transcript statistics and mapping completed.
Path:
CBEIPlot/Bacillus_subtilis_CDSlength.png
CBEIPlot/Bacillus_subtilis_GCstats.png
CBEIPlot/Bacillus_subtilis_CodonUsage.png
CBEIPlot/Bacillus_subtilis_CDSlength.png
The comparison of CBEI ratio of different BE has been completed.
Path:
CBEIPlot/Bacillus_subtilis.statBar.png
CBEIPlot/Bacillus_subtilis.statROC.png
CBEI statistics complete
4.2输出文件
输出目录或文件应为：
├── CBEIPlot
│ ├── BE-PLUS_Bacillus_subtilis.statPie.png
│ ├── BE_Bacillus_subtilis.statPie.png
│ ├── Bacillus_subtilis.statBar.png
│ ├── Bacillus_subtilis.statROC.png
│ ├── Bacillus_subtilis_CDSlength.png
│ ├── Bacillus_subtilis_CodonUsage.png
│ ├── Bacillus_subtilis_GCstats.png
│ ├── ...
├── CBEIRaw
│ ├── BE-PLUS_Bacillus_subtilis.part500.cds.all.fa.cbei
│ ├── BE_Bacillus_subtilis.part500.cds.all.fa.cbei
│ ├── ...
├── CBEIStat
│ ├── BE-PLUS_Bacillus_subtilis.Thre025.tsv
│ ├── BE-PLUS_Bacillus_subtilis.Thre05.tsv
│ ├── BE-PLUS_Bacillus_subtilis.Thre075.tsv
│ ├── ...
4.2.1.cbei文件格式
KDE22635 Minus 0.8674698795180723 {TGC,[TTT,C(C->T)]A,TAA,GAT,TAA,AA}|T,G TGCTTTCCATAAGATTAAAA 222-203 216,215 219-215 TG 201-202 TC,CC
- Fasta title: E.g., lacZ
- Strand: E.g., Plus
- Relative position: Edit position/Gene length. E.g., 0.012032520325203253
- Rich info: E.g., GT{C,GT[T,TTA,(C->T)]AA,CGT,CGT,GAC,T}|GG,G
- Spacer: E.g., CGTTTTACAACGTCGTGACT
- Spacer position: E.g., 30-49
- Edit position: E.g., 37
- Edit windows: E.g., 33-37
- PAM:E.g., GGG
- PAM position: E.g., 50-52
- Edit pattern: The edit pattern indicated the adjacent nucleotide at 5’ of the editable cytosine. Typically, the in vitro activity of the base editors follows TC ≥ CC ≥ AC > GC. E.g., AC
4.2.2.具有阈值的tsv文件
根据不同的阈值进行过滤。在
- Thre25: CBEI sites at the upsteam 25% of the CDS.
- Thre50: CBEI sites at the upsteam 50% of the CDS.
- Thre75: CBEI sites at the upsteam 75% of the CDS.
#Editable sites in the first 50% of the transcript
#Transcript Strand Position CBEIdetail Spacer SpacerRegion EditPosition EditWindowsRegion PAM PAMregion Pattern
KDE22636 Plus 0.3686274509803922 GG{A,TT[T,CTT,(C->T)]AA,CAA,ACA,GTA,C}|TG,G ATTTCTTCAACAAACAGTAC 87-106 94 90-94 TGG 107-109 TC
4.3图
Pie charts for different BEs have been generated.
Path:
./CBEIPlot/[BE names]_Bacillus_subtilis.statPie.tiff
Transcript statistics and mapping completed.
Path:
./CBEIPlot/Bacillus_subtilis_CDSlength.tiff
./CBEIPlot/Bacillus_subtilis_GCstats.tiff
./CBEIPlot/Bacillus_subtilis_CodonUsage.tiff
./CBEIPlot/Bacillus_subtilis_CDSlength.tiff
The comparison of CBEI ratio of different BE has been completed.
Path:
./CBEIPlot/Bacillus_subtilis.statBar.tiff
./CBEIPlot/Bacillus_subtilis.statROC.tiff
CBEI statistics complete
- 项目
标签：
欢迎加入QQ群-->： 979659372
