Conda installation problems: AttributeError: module 'os' has no attribute 'io'

[caity-s]

Hello,

I am excited to try AGB, I have been using bandage. The installation goes smoothly, and I can -h, however I get an error when I try to run the program. I made the conda env using Miniconda3 as described:

conda create -c almiheenko -c bioconda -n AGB agb
conda activate AGB
agb.py -i flye/ -a Flye
Extracting edge sequences from flye/assembly_graph.gfa...
No information about contig mappings to the reference genome
No information about edge mappings to the reference genome
Building JSON files...
Traceback (most recent call last):
  File "/shared-nfs/MGP1000/software/condaenvs/AGB/bin/agb.py", line 154, in <module>
    main()
  File "/shared-nfs/MGP1000/software/condaenvs/AGB/bin/agb.py", line 147, in main
    html = embed_css_and_scripts(html)
  File "/shared-nfs/MGP1000/software/condaenvs/AGB/lib/python3.6/site-packages/agb_src/scripts/utils.py", line 221, in embed_css_and_scripts
    with os.io.open(fpath, 'r', encoding="utf-8") as f: contents = f.read()
AttributeError: module 'os' has no attribute 'io'

agb.py --graph assembly_graph.gfa -a Flye
Parsing assembly_graph.gfa...
Finish parsing.
Extracting edge sequences from assembly_graph.gfa...
No information about contig mappings to the reference genome
No information about edge mappings to the reference genome
Building JSON files...
Traceback (most recent call last):
  File "/shared-nfs/MGP1000/software/condaenvs/AGB/bin/agb.py", line 154, in <module>
    main()
  File "/shared-nfs/MGP1000/software/condaenvs/AGB/bin/agb.py", line 147, in main
    html = embed_css_and_scripts(html)
  File "/shared-nfs/MGP1000/software/condaenvs/AGB/lib/python3.6/site-packages/agb_src/scripts/utils.py", line 221, in embed_css_and_scripts
    with os.io.open(fpath, 'r', encoding="utf-8") as f: contents = f.read()
AttributeError: module 'os' has no attribute 'io'

Should I install another piece of software?

Thank you,
Caity

[AnnaSyme]

Hi, I am having this same issue.

Installed with:

conda create -c almiheenko -c bioconda -n AGB agb

error:

agb.py -i flye-nohup/ -a flye 
Extracting edge sequences from flye-nohup/assembly_graph.gfa...
No information about contig mappings to the reference genome
No information about edge mappings to the reference genome
Building JSON files...
Traceback (most recent call last):
  File "/home/anna/miniconda3/envs/AGB/bin/agb.py", line 154, in <module>
    main()
  File "/home/anna/miniconda3/envs/AGB/bin/agb.py", line 147, in main
    html = embed_css_and_scripts(html)
  File "/home/anna/miniconda3/envs/AGB/lib/python3.6/site-packages/agb_src/scripts/utils.py", line 221, in embed_css_and_scripts
    with os.io.open(fpath, 'r', encoding="utf-8") as f: contents = f.read()
AttributeError: module 'os' has no attribute 'io'

This seems to be the same or similar issue to @TomHarrop
#3 (comment)?

Many thanks if any ideas!

Anna

[almiheenko]

This issue should be fixed by now, thanks to @kbseah.
Conda package is updated.