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asntech / intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
http://intervene.rtfd.io/
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After upgrade to pandas 1.0.0, DataFrame.ix is removed #37

Closed yulijia closed 3 years ago

yulijia commented 3 years ago

Hi,

I installed the intervene package with pip command, this is a real nice and useful tool.

However, I find that if the users try to generate a pairwise plot with pandas version 1.0.0, the software will throw an error message AttributeError: 'DataFrame' object has no attribute 'ix'.

.ix is deprecated in the newest pandas package.

Could you mind updating the intervene package with the new attribute: use .iloc or .loc instead of .ix at https://github.com/asntech/intervene/blob/master/intervene/modules/pairwise/pairwise.py#L150 and https://github.com/asntech/intervene/blob/master/intervene/modules/pairwise/pairwise.py#L214

D = D.iloc[cluster_order, cluster_order] is for number indexing series = series.loc[order] is for str indexing

Thanks, Lijia

bioinfouser commented 3 years ago

Hi Lijia, I am not the owner of intervene, but it works with python 2.7. Just make a new conda environment and reinstall. It should run. Best,

yulijia commented 3 years ago

The same issue posted at #40

asntech commented 3 years ago

Hi @yulijia, Please check it now and try to install it from the source. I will make available an updated version through bioconda and pip soon.

yulijia commented 3 years ago

Thank you, it works now.