设计和分析CRISPRi实验的工具
crisprbact的Python项目详细描述
脆肉
设计和分析细菌CRISPRi实验的工具。
CRISPRbact目前包含一个化脓性链球菌dCas9蛋白的靶向活性预测工具。 此工具将感兴趣基因的序列作为输入，并返回一个可能的目标序列列表，其中包含预测的靶向活性。使用线性模型对大肠杆菌全基因组CRISPRi筛查数据进行预测（Cui等人，《自然通讯》，2018年）。该模型预测了当靶基因的非模板链（即编码链）靶向时，dCas9阻断RNA聚合酶的能力。在
入门
安装
目前，您只能通过PyPI安装这个包
PyPI
$ pip install crisprbact $ crisprbact --help^{pr2}$
API
在python代码中使用这个库。在
fromcrisprbactimporton_target_predictguide_rnas=on_target_predict("ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG")forguide_rnainguide_rnas:print(guide_rna)
输出：
{'target': 'TCATCACGGGCCTTCGCCACGCGCG', 'guide': 'TCATCACGGGCCTTCGCCAC', 'start': 82, 'stop': 102, 'pam': 80, 'ori': '-', 'target_id': 1, 'pred': -0.4719254873780802, 'off_targets_per_seed': []}
{'target': 'CATCACGGGCCTTCGCCACGCGCGC', 'guide': 'CATCACGGGCCTTCGCCACG', 'start': 81, 'stop': 101, 'pam': 79, 'ori': '-', 'target_id': 2, 'pred': 1.0491308060379676, 'off_targets_per_seed': []}
{'target': 'CGCGCGCGGCAAACAATCACAAACA', 'guide': 'CGCGCGCGGCAAACAATCAC', 'start': 63, 'stop': 83, 'pam': 61, 'ori': '-', 'target_id': 3, 'pred': -0.9021152826078697, 'off_targets_per_seed': []}
{'target': 'CCTGATCGGTATTGAACAGCATCTG', 'guide': 'CCTGATCGGTATTGAACAGC', 'start': 29, 'stop': 49, 'pam': 27, 'ori': '-', 'target_id': 4, 'pred': 0.23853258873311955, 'off_targets_per_seed': []}
命令行界面
预测指南RNAs活性
输入一个目标基因的序列，这个脚本将输出化脓链球菌dCas9的候选指导rna，并预测靶活性。在
$ crisprbact predict --help
Usage: crisprbact predict [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Commands:
from-seq Outputs candidate guide RNAs for the S.
from-str Outputs candidate guide RNAs for the S.
来自字符串序列：
目标输入序列可以是一个简单的字符串。在
$ crisprbact predict from-str --help
Usage: cli.py predict from-str [OPTIONS] [OUTPUT_FILE]
Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-
target activity from a target gene.
[OUTPUT_FILE] file where the candidate guide RNAs are saved. Default =
"stdout"
Options:
-t, --target TEXT Sequence file to target [required]
-s, --off-target-sequence FILENAME
Sequence in which you want to find off-
targets
-w, --off-target-sequence-format [fasta|gb|genbank]
Sequence in which you want to find off-
targets format [default: genbank]
--help Show this message and exit.
$ crisprbact predict from-str -t ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG guide-rnas.tsv
输出文件guide-rnas.tsv：
没有定义seq_id，因为它来自一个简单的字符串。在
target PAM position prediction seq_id
TCATCACGGGCCTTCGCCACGCGCG 80 -0.4719254873780802 N/A
CATCACGGGCCTTCGCCACGCGCGC 79 1.0491308060379676 N/A
CGCGCGCGGCAAACAATCACAAACA 61 -0.9021152826078697 N/A
CCTGATCGGTATTGAACAGCATCTG 27 0.23853258873311955 N/A
也可以通过管道传输结果：
$ crisprbact predict from-str -t ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG | tail -n +2 | wc -l
来自序列文件
$ crisprbact predict from-seq --help
Usage: cli.py predict from-seq [OPTIONS] [OUTPUT_FILE]
Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-
target activity from a target gene.
[OUTPUT_FILE] file where the candidate guide RNAs are saved. Default =
"stdout"
Options:
-t, --target FILENAME Sequence file to target [required]
-f, --seq-format [fasta|gb|genbank]
Sequence file to target format [default:
fasta]
-s, --off-target-sequence FILENAME
Sequence in which you want to find off-
targets
-w, --off-target-sequence-format [fasta|gb|genbank]
Sequence in which you want to find off-
targets format [default: genbank]
--help Show this message and exit.
- Fasta文件（可以是multifasta文件）
$ crisprbact predict from-seq -t /tmp/seq.fasta guide-rnas.tsv
- GenBank文件
$ crisprbact predict from-seq -t /tmp/seq.gb -f gb guide-rnas.tsv
- 偏离目标
predict from-seq -t data-test/sequence.fasta -s data-test/sequence.gb guide-rnas.tsv输出文件
target_id target PAM position prediction target_seq_id seed_size off_target_recid off_target_start off_target_end off_target_pampos off_target_strand off_target_feat_type off_target_feat_start off_target_feat_end off_target_feat_strand off_target_locus_tag off_target_gene off_target_note off_target_product off_target_protein_id
1 TGATCCAGGCATTTTTTAGCTTCAT 835 0.47949500169043713 NC_017634.1:2547433-2548329 8 NC_017634.1 1388198 1388209 1388209 +
1 TGATCCAGGCATTTTTTAGCTTCAT 835 0.47949500169043713 NC_017634.1:2547433-2548329 8 NC_017634.1 2244514 2244525 2244525 + CDS 2243562 2244720 -1 NRG857_10810 COG1174 ABC-type proline/glycine betaine transport systems, permease component putative transport system permease YP_006120510.1
1 TGATCCAGGCATTTTTTAGCTTCAT 835 0.47949500169043713 NC_017634.1:2547433-2548329 8 NC_017634.1 4160984 4160995 4160995 + CDS 4160074 4161406 -1 NRG857_19625 hslU COG1220 ATP-dependent protease HslVU (ClpYQ), ATPase subunit ATP-dependent protease ATP-binding subunit HslU YP_006122267.1
1 TGATCCAGGCATTTTTTAGCTTCAT 835 0.47949500169043713 NC_017634.1:2547433-2548329 8 NC_017634.1 4534189 4534200 4534200 +
1 TGATCCAGGCATTTTTTAGCTTCAT 835 0.47949500169043713 NC_017634.1:2547433-2548329 8 NC_017634.1 548804 548815 548804 -
1 TGATCCAGGCATTTTTTAGCTTCAT 835 0.47949500169043713 NC_017634.1:2547433-2548329 8 NC_017634.1 786462 786473 786462 - CDS 785384 786470 1 NRG857_03580 COG2055 Malate/L-lactate dehydrogenases hypothetical protein YP_006119079.1
贡献
克隆回购
$ git clone https://gitlab.pasteur.fr/dbikard/crisprbact.git
创建一个virtualenv
$ virtualenv -p python3.7 .venv $ . .venv/bin/activate $ pip install poetry
安装CrispBarct依赖项
$ poetry install
安装挂钩
为每次提交运行flake8和black。在
^{pr21}$- 项目
标签：
欢迎加入QQ群-->： 979659372
