hua-cm / huasmalltools Goto Github PK

你好,非常感谢您的开源教程, 我在根据eggnog-mapper在线注释结果进行GO、KEGG分析时, 有一个疑问关于您教程中提到 需要首先需要去GO下载GO的obo文件,并使用go-basic.obo脚本可以对obo文件解析. 我不太清楚为什么不能直接根据eggnog-mapper结果中的注释信息通过enrichr函数绘图, 这里下载GO的obo文件的作用是?

希望得到您的指导:

你好，我在使用您提供的脚本对EggNOG注释的结果进行GO和KEGG提取使出现了错误：命令行是：
python parse_eggNOG.py -i ../query_seqs.fa.emapper.annotations -g go.tb -O ath,osa -o result
出现了以下的报错：
Traceback (most recent call last):
File "parse_eggNOG.py", line 133, in
main(args.input_file, args.output_directory, args.go_file, args.org_list.split(","))
File "parse_eggNOG.py", line 114, in main
file4KO = parse_KO(file4parse, org_list)[["gene", "KO", "pathway", "description"]]
File "parse_eggNOG.py", line 81, in parse_KO
KO2map, KEGGmap = get_KEGGmap(own_mapdb(org_list))
File "parse_eggNOG.py", line 35, in own_mapdb
tmp_df = pd.DataFrame(tmp, columns=["pathway", "description"]).dropna()
File "/lustre/xzq/miniconda3/lib/python3.6/site-packages/pandas/core/frame.py", line 407, in init
raise TypeError("data argument can't be an iterator")

请问这怎么解决，谢谢！

eggNOG更新了它的输出文件格式，这个脚本可能不适合现在的格式了
(R) [lihr@localhost cultivar_Lee]$ python ../HuaSmallTools-master/parse/parse_eggNOG.py -i out.emapper.annotations -g go.tb -O gmx -o cultivar_Lee
Traceback (most recent call last):
File "../HuaSmallTools-master/parse/parse_eggNOG.py", line 134, in
main(args.input_file, args.output_directory, args.go_file, args.org_list.split(","))
File "../HuaSmallTools-master/parse/parse_eggNOG.py", line 117, in main
file4KO.to_csv(os.path.join(out_dir, "KOannotation.tsv"), sep="\t", index=False)
File "/home/lihr/software/miniconda3/envs/R/lib/python3.8/site-packages/pandas/core/generic.py", line 3170, in to_csv
formatter.save()
File "/home/lihr/software/miniconda3/envs/R/lib/python3.8/site-packages/pandas/io/formats/csvs.py", line 185, in save
f, handles = get_handle(
File "/home/lihr/software/miniconda3/envs/R/lib/python3.8/site-packages/pandas/io/common.py", line 493, in get_handle
f = open(path_or_buf, mode, encoding=encoding, errors=errors, newline="")
FileNotFoundError: [Errno 2] No such file or directory: 'cultivar_Lee/KOannotation.tsv'

非常不好意思，想请问一下这个问题应该怎么解决。
输入为：python parse_eggNOG.py -i MM.emapper.annotations.tsv -g go.tb -O spar,pti,fcy,tps -o test
报错为：
Traceback (most recent call last):
File "parse_eggNOG.py", line 154, in
main(args.input_file, args.output_directory, args.go_file, args.org_list.split(","))
File "parse_eggNOG.py", line 131, in main
usecols=check_column(input_file),
File "parse_eggNOG.py", line 124, in check_column
return 0, go_idx, kegg_idx
UnboundLocalError: local variable 'go_idx' referenced before assignment