error with add_annotation_from_dat.py

[Wanliwill]

Hi,
When I run ：python add_annotation_from_dat.py expanded_dup.blastp.best uniprot_plants.dat
there is such an error：
Traceback (most recent call last):
File "add_annotation_from_dat.py", line 22, in
GO_RECORD = re.findall(r"GO; (GO:\d+); ([F|P|C]):.?; (.):",record)
File "/pub/anaconda3/envs/py36/lib/python3.6/re.py", line 222, in findall
return _compile(pattern, flags).findall(string)
TypeError: cannot use a string pattern on a bytes-like object

I do not know what is wrong, please help, thank you very much

[lin0yuan]

Hi, I also got a similar error message when I run "python3 add_annotation_from_dat.py BRA1306.matches.m6.best uniprot_invertebrates.dat"

Traceback (most recent call last):
File "add_annotation_from_dat.py", line 22, in
GO_RECORD = re.findall(r"GO; (GO:\d+); ([F|P|C]):.?; (.):",record)
File "/usr/lib/python3.8/re.py", line 241, in findall
return _compile(pattern, flags).findall(string)
TypeError: cannot use a string pattern on a bytes-like object

Would you mind giving some suggestions? Thanks a lot!

[Wanliwill]

I don't know how to solve it either, and I eventually gave up using this script.

[lin0yuan]

Hi there @Wanliwill, I successfully got rid of the error by adding a line "record = record.decode(‘utf-8’)". Maybe you can have a try.

if not uniprot.get(acc.strip(";")):
    continue
record = uniprot.get_raw(acc.strip(";"))

# need to add a command here to tackle with the unicode string inconsistency between python2 and python3
record = record.decode(‘utf-8’)

GO_RECORD = re.findall(r"GO; (GO:\d+); ([F|P|C]):.*?; (.*):",record)

[Wanliwill]

Great. I'll give it a try. Thank you so much