pyranges: left join broken with ValueError and TypeError

Thanks for the package- and all the hard work that’s gone into it. Came across this issue:

f1 = pr.from_dict(
  {'Chromosome': ['chr1', 'chr1', 'chr1'], 
   'Start': [3, 8, 12],
   'Strand': ['+', '-', '+'],
   'End': [4, 9, 13], 
   'Name': ['interval1', 'interval3', 'interval2']
}, int64=True)

f2 = pr.from_dict(
  {
    'Chromosome': ['chr1'], 
    'Start': [6], 
    'Strand': ['-'],
    'End': [10], 
    'GeneName': ['test']
}, int64=True)

I’m trying to annotate f1 with f2.

f3 = f1.join(f2, strandedness="same", slack=0)

works as expected

f3 = f1.join(f2, how="left", strandedness="same", slack=0)

Fails with an error TypeError: Cannot set a Categorical with another, without identical categories

Version is '0.0.125

About this issue

  • Original URL
  • State: closed
  • Created a year ago
  • Comments: 22 (3 by maintainers)

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I’ll try to fix this today. Will have to check on different pandas versions 😄