changeO

参考：https://changeo.readthedocs.io/en/stable/examples/igblast.html
安装changeO

conda create -n changeo
conda activate changeo
conda install python=3.8.0
pip3 install changeo

wget ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.18.0/ncbi-igblast-1.18.0-x64-linux.tar.gz
tar zxvf ncbi-igblast-1.18.0-x64-linux.tar.gz
把ncbi-igblast-1.18.0/bin/的script加入环境变量

前期数据准备：

1. 从这里下载脚本scripts：https://bitbucket.org/kleinstein/immcantation/downloads/，这些脚本目录是kleinstein-immcantation-40b86f83caa1/scripts/，把scripts加入环境变量
2. IMGT文件下载：https://www.imgt.org/download/V-QUEST/IMGT_V-QUEST_reference_directory/

mkdir /path/to/software/changeO
cd changeO
# Download reference databases and setup IGDATA directory
kleinstein-immcantation-40b86f83caa1/scripts/fetch_igblastdb.sh -o igblast
cp -r ncbi-igblast-1.18.0/internal_data igblast
cp -r ncbi-igblast-1.18.0/optional_file igblast

# Build IgBLAST database from IMGT reference sequences
kleinstein-immcantation-40b86f83caa1/scripts/fetch_imgtdb.sh -o germlines/imgt
kleinstein-immcantation-40b86f83caa1/scripts/imgt2igblast.sh -i germlines/imgt -o igblast

正式跑change-O

AssignGenes.py igblast --outdir ./ --outname CRC_PS017_T --nproc 20 -s ../CRC_PS017_T_annot.fa --organism human -b /data/workdir/wubq/soft/changeO/igblast/