跟着以前的教程做了很久,在conda里面安装卸载安装卸载好几次,每次激活环境之后都是显示
-bash: cellphonedb: command not found
去问gpt也是说cellphonedb是可以通过命令行进行交互的。
但是github上面说明文档里面的示例是用python写的:
from cellphonedb.src.core.methods import cpdb_degs_analysis_method
cpdb_results = cpdb_degs_analysis_method.call(
cpdb_file_path = cellphonedb.zip,
meta_file_path = test_meta.txt,
counts_file_path = test_counts.h5ad,
degs_file_path = degs_file_path,
counts_data = 'hgnc_symbol',
active_tfs_file_path = active_tf.txt,
score_interactions = True,
microenvs_file_path = microenvs_file_path,
threshold = 0.1,
output_path = out_path)
而之前的版本,示例代码是这样:
cellphonedb method statistical_analysis test_meta.txt test_counts.txt
尝试了一下,用python3.6环境安装3.0.0版本的cellphonedb,安装完成后输入cellphonedb,回车,显示:
Usage: cellphonedb [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Commands:
database
method
plot
query
所以就是版本问题了……5.0.0版本不能直接用命令行交互了……因为这个折腾了一晚上,麻了。