Package versions

[inari-ldavey]

Hi, could you provide the versions of the python packages that were used for the analysis? I'm trying to recreate the analysis in CNN/model_train+evaluate.ipynb, but I get an error on this cell:

term_SeqData = eu.dl.SeqData(
  seqs = data_term['sequence'],
  names = data_term.index,
  seqs_annot = data_term[['enrichment_tobacco', 'enrichment_maize', 'set', 'species']]
)
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[11], line 1
----> 1 term_SeqData = eu.dl.SeqData(
      2   seqs = data_term['sequence'],
      3   names = data_term.index,
      4   seqs_annot = data_term[['enrichment_tobacco', 'enrichment_maize', 'set', 'species']]
      5 )

AttributeError: module 'eugene' has no attribute 'dl'

I suspect this is because an older version of eugene was used

[lampoona]

can you add: "from package eugene import dl" before running this portion and see if it imports? It's probably a package issue.

If you want to bypass this, you could write your own dataloader to create a SeqData object to work with. Here is the screenshot from the eugene manaul to assist:

[inari-ldavey]

I didn't have eugene-tools v0.0.6 properly installed