Description
Hi,
I ran pyscenic successfully up to df2regulons() step and saved the result into pickle file. When I open the pickle file and try to access the gene names in each regulon, I get this weird formatting error. I don't know how to resolve this. I pasted the script and the output.
The script
with open(REGULONS, 'rb') as file:
regulons = pickle.load(file)
print(type(regulons))
print(len(regulons))
first = regulons[0]
print(type(first))
print(dir(first))
print(first.name)
print(first.transcription_factor)
print(first.genes) # Output is weird because somehow it's printing out each character
The output
<class 'list'>
255
<class 'ctxcore.genesig.Regulon'>
['__annotations__', '__attrs_attrs__', '__class__', '__contains__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__getitem__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__len__', '__lt__', '__match_args__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__slots__', '__str__', '__subclasshook__', '__weakref__', 'add', 'annotation', 'context', 'copy', 'difference', 'from_gmt', 'from_grp', 'from_rnk', 'from_yaml', 'gene2occurrence', 'gene2weight', 'gene2weight_validator', 'genes', 'head', 'intersection', 'jaccard_index', 'metadata', 'name', 'name_validator', 'nes', 'non_empty', 'noweights', 'orthologous_identity', 'rename', 'score', 'similarity_qvalue', 'to_gmt', 'to_yaml', 'transcription_factor', 'union', 'weights', 'yaml_dumper', 'yaml_flow_style', 'yaml_loader', 'yaml_tag']
Arid3a(+)
Arid3a
('[', '(', "'", 'O', 's', 'g', 'i', 'n', '1', ',', ' ', 'p', '.', 'f', 'l', 'o', 'a', 't', '6', '4', '0', '5', '2', '9', '3', ')', 'D', 'd', 'x', '8', 'I', '7', 'A', 'r', 'b', ']')
So instead of readable gene names, I get this: ('[', '(', "'", 'O', 's', 'g', 'i', 'n', '1', ',', ' ', 'p', '.', 'f', 'l', 'o', 'a', 't', '6', '4', '0', '5', '2', '9', '3', ')', 'D', 'd', 'x', '8', 'I', '7', 'A', 'r', 'b', ']')
Does anyone have similar issue? Can anyone please help me?
Thank you.
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