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ma-compbio / Phylo-HMRF

MIT License
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AttributeError: 'module' object has no attribute 'cut_general_graph' #7

Open nt365 opened 4 years ago

nt365 commented 4 years ago

Hello,

I am having trouble with the pygco installation. I attempted all of the various suggestions for installation including pip install gco-wrapper which appeared to work successfully. I installed the wrapper with the following: pip install -r requirements.txt python setup.py install and this said it installed the dependencies successfully.

However, when I run the example for phylohmrf I keep getting the attached error. Command: python phylo_hmrf.py -n 20 -r 1 --reload 0 --chromvec 21,22 --miter 100 -p ./example_input/ phylohmrf_gco_error.txt

Any feedback into how to solve this issue would be appreciated.

Thank you, Nicole

yangymargaret commented 4 years ago

Hi Nicole @nt365, Thank you very much for your interest in Phylo-HMRF. I do apologize for the delay in my reply. Would you please try installing pygco from the source code? Please refer to the instructions in https://github.com/yujiali/pygco to install pygco. If you could not find gco_source from the original link referred to, you could use the source code in the gco_source file folder contained within this repository. There is a copy of the source code of GCO in ./gco_source. Please see the descriptions in the section 'Required pre-installed packages'. After you have installed pygco, please try 'import pygco' in Python. If it works, then please see if running the example command can work.

Please let me know if this helps or if you have any other questions. Many thanks!

Best regards! Yang Yang

nt365 commented 4 years ago

Sorry for the delay,

I was able to make it work by replacing line 496 from "labels=pygco.cut_general_graph" to "labels=gco.cut_general_graph".

Thank you! Nicole