max_clusters error

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Peter Ulintz

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Oct 30, 2018, 8:57:35 AM10/30/18
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Hello, I'm getting the following error when trying to generate the loci table or plots on a result set:


(PyClone) CRC14_1509-subset2$ PyClone --version

PyClone-0.13.1


(PyClone) CRC14_1509-subset2$ PyClone build_table --config_file config_crc14_1509-subset2.yaml --table_type loci --out_file tables/CRC14-1509-subset2.loci.table.txt

Traceback (most recent call last):

  File "/Users/pulintz/Packages/anaconda3/envs/PyClone/bin/PyClone", line 11, in <module>

    load_entry_point('PyClone==0.13.1', 'console_scripts', 'PyClone')()

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/cli.py", line 78, in main

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/run.py", line 348, in build_table

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/run.py", line 368, in _build_table

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/post_process/loci.py", line 31, in load_table

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/post_process/clusters.py", line 30, in cluster_pyclone_trace

TypeError: cluster_with_mpear() got an unexpected keyword argument 'max_clusters'


(PyClone) CRC14_1509-subset2$ PyClone plot_clusters --config_file config_crc14_1509-subset2.yaml --plot_type parallel_coordinates --plot_file plots/config_crc14_1509-subset2.clusters.freqs.line.png --min_cluster_size 3 --max_clusters 50

Traceback (most recent call last):

  File "/Users/pulintz/Packages/anaconda3/envs/PyClone/bin/PyClone", line 11, in <module>

    load_entry_point('PyClone==0.13.1', 'console_scripts', 'PyClone')()

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/cli.py", line 78, in main

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/run.py", line 393, in cluster_plot

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/run.py", line 422, in _cluster_plot

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/post_process/plot/clusters.py", line 150, in parallel_coordinates_plot

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/post_process/clusters.py", line 48, in load_summary_table

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/post_process/clusters.py", line 98, in load_table

  File "build/bdist.macosx-10.9-x86_64/egg/pyclone/post_process/clusters.py", line 30, in cluster_pyclone_trace

TypeError: cluster_with_mpear() got an unexpected keyword argument 'max_clusters'



Any suggestions?

Thanks,
Pete

Andrew

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Apr 18, 2019, 12:20:10 PM4/18/19
to Pyclone User Group
The PyDP install is out of date. Try getting the latest version from the git repo https://github.com/aroth85/pydp.
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