cDNA_Cupcake-安装

Cupcake是一个三代测序后续分析软件的集合,其中包含的ToFu软件可进行转录本的修剪（collapse_isoforms_by_sam.py）以及融合基因（fusion_finder.py）的鉴定。

下载Cupcake

git clone https://github.com.cnpmjs.org/Magdoll/cDNA_Cupcake.git
cd cDNA_Cupcake/

Tofu软件不能直接使用，需要安装，需要python>=3.7

创建conda环境

conda create -n python37 python=3.7
conda activate python37
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --set show_channel_urls yes
pip install pip -U
pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple

安装依赖包

pip install numpy
pip install Cython
python setup.py build
python setup.py install

整个安装过程大概十几分钟
最后测试一下

$collapse_isoforms_by_sam.py -h
usage: collapse_isoforms_by_sam.py [-h] [--input INPUT] [--fq] [-s SAM]
                                   [-b BAM] -o PREFIX [-c MIN_ALN_COVERAGE]
                                   [-i MIN_ALN_IDENTITY]
                                   [--max_fuzzy_junction MAX_FUZZY_JUNCTION]
                                   [--max_5_diff MAX_5_DIFF]
                                   [--max_3_diff MAX_3_DIFF]
                                   [--flnc_coverage FLNC_COVERAGE]
                                   [--gen_mol_count] [--dun-merge-5-shorter]
                                   [--cpus CPUS]
$fusion_finder.py 
usage: fusion_finder.py [-h] [--input INPUT] [--fq] -s SAM -o PREFIX
                        [--cluster_report_csv CLUSTER_REPORT_CSV] [--is_flnc]
                        [--dun-merge-5-shorter] [-c MIN_LOCUS_COVERAGE]
                        [--min_locus_coverage_bp MIN_LOCUS_COVERAGE_BP]
                        [-t MIN_TOTAL_COVERAGE] [-d MIN_DIST_BETWEEN_LOCI]
                        [-i MIN_IDENTITY]

更多用途需要探索，后续更新