sequence-finder:在细菌基因组中搜索物种特定区域

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  • 2022-06-15 09:42
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序列查找器 小型快速Python管道,用于搜索细菌基因组中特定于物种的区域。 要求 您需要安装: 高炉- conda install -c bioconda blast 安装 克隆回购 git clone git@github.com:polinchen98/sequence-finder.git 安装套件 pip intall -r requirements.txt 如果这在旧版本的Python上失败,请尝试首先更新您的pip工具: pip install --upgrade pip 用法 prepare.py下载和创建数据库(正负) python prepare.py --genus pectobacterium --species parmentieri --id CP015749.1 splitter.py具有指定间隔和长度的分割序列 python splitter.p
sequence-finder-master.zip
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  • prepare.py
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  • blast.py
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  • requirements.txt
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  • splitter.py
    1019B
  • README.md
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内容介绍
# Sequence finder Small fast Python pipeline for searching species-specific regions in bacterial genomes. ### Requirements You need have installed: - [bioconda](https://bioconda.github.io/user/install.html) - Blast - `conda install -c bioconda blast` ### Installation Clone repo `git clone git@github.com:polinchen98/sequence-finder.git` Install packages `pip intall -r requirements.txt` If this fails on older versions of Python, try updating your `pip` tool first: `pip install --upgrade pip` ### Usage `prepare.py` - downloading and creating databases(positive and negative) `python prepare.py --genus pectobacterium --species parmentieri --id CP015749.1` --- `splitter.py` - split sequence with a specified interval and length `python splitter.py` file_sequence: - `/path/to/file` Length sequence: - length of fragment (e.g 100) interval: - step (e.g 10) --- `blast.py` - compares splitted genome with the selected database and creates two files: `hits.fna` and `no_hits.fna` `python blast.py --input path/to/input_file.fna --db path/to/blast_database_folder`
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