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KrATER的Python项目详细描述
#krater（k-mer分析工具易于运行）
要求
- Python libraries:
- Matplotlib Numpy Scipy
- Jellyfish 2
安装
- 安装要求
从http://www.genome.umd.edu/jellyfish.html安装水母2.x.x
- 安装python库（如果要通过pip安装krater，则不需要）
运行以下命令进行全局安装
sudo pip install matplotlib numpy scipy
如果您没有根权限，请执行以下本地安装命令
pip install –user matplotlib numpy scipy
- 安装krater
变体1：使用pip安装
run following command for global installation
sudo pip install krater
运行以下命令进行本地安装
pip install –user krater
然后在路径变量中添加~/.local/bin
cat “PATH=${PATH}:~/.local/bin/” >> ~/.profile cat “PATH=${PATH}:~/.local/bin/” >> ~/.bashrc
加载更新的路径变量
source ~/.profile
变量2：从具有根权限的源代码安装
git clone https://github.com/mahajrod/krater cd krater python setup.py build sudo python setup.py install
变量3：从没有根权限的源代码安装
- Get KRATER
git clone https://github.com/mahajrod/krater
Add following strings to ~/.profile and ~/.bashrc (create files if absent). Don’t forget to replace <KRATER_DIR> with actual path
PYTHONPATH=${PYTHONPATH}:<KRATER_DIR> PATH=${PATH}:<KRATER_DIR> export PYTHONPATH export PATH
- 磨合终端
源~/.profile
运行
If input file/files is/are fastq:
- Typical usage:
draw_kmer_distribution_from_fastq.py -m 23 -t ${THREAD_NUMBER} -b -s 30G -e png -o ${OUTPUT_PREFIX} -i {COMMA_SEPARATED_LIST_OF_FASTQ_FILES} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE}
Parameter description:
如果输入文件是水母数据库
- Typical usage:
draw_kmer_distribution_from_jellyfish_database.py -i ${JELLYFISH_DATABASE} -o ${OUTPUT_PREFIX} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -e png
如果输入文件是由水母生成的直方图文件：
- Typical usage
draw_kmer_distribution_from_histo.py -i ${JELLYFISH_HISTO_FILE} -o ${OUTPUT_PREFIX} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -e png
Parameter_description:
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