ValueError: invalid mode: 'rU' when running emapper.py with the --md5 option

[samuelruizperez]

Hi!

After installing eggnog-mapper v2.1.9 through conda (Python 3.11.0) and running emapper.py with the --md5 option I got this error:

Creating md5 hashes of input sequences

Parsing fasta file /path/to/proteins.fa...

Traceback (most recent call last):
  File "/home/usr/.conda/envs/env_name/bin/emapper.py", line 704, in <module>
    n, elapsed_time = emapper.run(args, args.input, args.annotate_hits_table, args.cache_file)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/usr/.conda/envs/env_name/lib/python3.11/site-packages/eggnogmapper/emapper.py", line 342, in run
    annotated_hits = self.annotate(args, hits, annotate_hits_table, queries_file, cache_dir)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/usr/.conda/envs/env_name/lib/python3.11/site-packages/eggnogmapper/emapper.py", line 232, in annotate
    annotated_hits = annotator.annotate(annot_in,
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/usr/.conda/envs/env_name/lib/python3.11/site-packages/eggnogmapper/annotation/annotator.py", line 108, in annotate
    md5_queries = md5_seqs(queries_file, translate, self.trans_table)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/usr/.conda/envs/env_name/lib/python3.11/site-packages/eggnogmapper/annotation/annotator.py", line 407, in md5_seqs
    for name, seq in iter_fasta_seqs(fasta_file, translate=translate, trans_table=trans_table):
  File "/home/usr/.conda/envs/env_name/lib/python3.11/site-packages/eggnogmapper/search/hmmer/hmmer_seqio.py", line 26, in iter_fasta_seqs
    _source = open(source, "rU")
              ^^^^^^^^^^^^^^^^^^
ValueError: invalid mode: 'rU'

I'm not sure if this is the correct place to post this bug, but I guess the problem is that the 'U' option is the default behavior of the open() function since Python 3.0, and it was deprecated in Python 3.11. I removed the 'U' from _source = open(source, "rU") and it is working fine.

Thanks!

[Cantalapiedra]

Hi @samuelruizperez ,

Thank you for reporting this.
Did you try with a python version previous to 3.11?

[samuelruizperez]

Yes! Works fine with Python 3.9.15.

[Cantalapiedra]

Thank you Samuel! And sorry for the headaches

[Cantalapiedra]

This should be fixed in version 2.1.10.
Please, re-open if needed.

[taylorreiter]

I encountered this error with mode --translate, also fixed by downgrading python. I think it might be from this line of code:

eggnog-mapper/eggnogmapper/utils.py

Line 233 in 69c8afd

_source = open(source, "rU")

[Cantalapiedra]

Thank you very much!
We will try to fix it ASAP