AttributeError: module 'iphop.modules.blast_genomes' has no attribute 'run_and_parse_blast_to_host'

[Karen Jin]

Traceback (most recent call last):
  File "/storage/jufengLab/jinlingrong/Software/miniconda3/envs/iphop/bin/iphop", line 8, in <module>
    sys.exit(cli())
  File "/storage/jufengLab/jinlingrong/Software/miniconda3/envs/iphop/lib/python3.8/site-packages/iphop/iphop.py", line 128, in cli
    args["func"](args)
  File "/storage/jufengLab/jinlingrong/Software/miniconda3/envs/iphop/lib/python3.8/site-packages/iphop/modules/master_predict.py", line 76, in main
    blast_genomes.run_and_parse_blast_to_host(args)
AttributeError: module 'iphop.modules.blast_genomes' has no attribute 'run_and_parse_blast_to_host'

When running iphop predict, I got the above error message. It seems that the “blast_genomes.py” file is empty. Can you fix this issue?

[Simon Roux]

Hi,

This is quite strange, and suggests an issue during the install process. It looks like you tried to install via conda, can you try again in a new environment, and can you also check if you have enough space in this directory (/storage/jufengLab/jinlingrong/Software/miniconda3/envs/) ?

[Karen Jin]

I installed by cloning the git repo. I found that the “blast_genomes.py” file is empty at the git repo: https://bitbucket.org/srouxjgi/iphop/src/main/iphop/modules/ I tried to fix the issue by copying and pasting an earlier version of “blast_genomes.py” and it worked for now. Just wanted to raise the issue as it seems to me that the last git commit “Fixed a warning in blast parsing that was confusing and useless when processing a custom database” deleted all the code.

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[Simon Roux]

Yikes you’re right, something went very wrong, thanks a lot for letting me know ! I’ll look into it asap.

[Simon Roux]

Should be fixed now, thanks again for reporting ! I’m closing the issue for now as everything should work, but please don’t hesitate to re-open if you notice anything. Note that for your own analysis, you don’t need to update to the latest commit, these latest changes are only cosmetic.

[Simon Roux]

Should be fixed now