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Roth-Lab / pyclone-vi

Fast method for inferring cancer clonal population structure from SNV data.
GNU General Public License v3.0
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Data loading issue #22

Open mda-hillmanlab opened 2 years ago

mda-hillmanlab commented 2 years ago

When running pyclone-vi for the first time, I created a dataset based on the usage instructions (see attached file: pyclone_test.txt). I then run the following command, adapted from the vigenette: pyclone-vi fit -i pyclone_test.txt -o pyclone_test.h5 -c 40 -d beta-binomial -r 10

This produces the following output and errors. As far as I can tell, my data are formatted identically to the example file "tracerx.tsv", and things run fine when I use that file as input.

Removing 3 mutations with major copy number zero

Traceback (most recent call last): File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/bin/pyclone-vi", line 8, in sys.exit(main()) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/click/core.py", line 1130, in call return self.main(args, kwargs) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/click/core.py", line 760, in invoke return __callback(args, kwargs) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/pyclone_vi/cli.py", line 113, in fit pyclone_vi.run.fit(kwargs) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/pyclone_vi/run.py", line 29, in fit log_p_data, mutations, samples = load_data(in_file, density, num_grid_points, precision=precision) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/pyclone_vi/data.py", line 11, in load_data data, mutations, samples = load_pyclone_data(file_name) File "/rsrch3/home/gyn_onc_rep_med/rthillman/.conda/envs/pyclone-vi/lib/python3.10/site-packages/pyclone_vi/data.py", line 78, in load_pyclone_data cn, mu, log_pi = cn_priors[( TypeError: unhashable type: 'Series'

jbedo commented 2 years ago

I encountered this, was due to multiple mutant ids as pointed out in #12.

edceeyuchen commented 1 year ago

I encountered this, was due to multiple mutant ids as pointed out in #12.

@jbedo ，Hello, jebdo, I met this problem, but I don't understand #12 answers? It's the problem about mutation_id col?

jbedo commented 1 year ago

Sorry this was a while ago so I don't quite remember, it might be that I encountered this error when mutation_id and sample_id didn't form a candidate key.

edceeyuchen commented 1 year ago

Sorry this was a while ago so I don't quite remember, it might be that I encountered this error when mutation_id and sample_id didn't form a candidate key.

Thank you very much for your prompt reply. I have solved this problem by modifying mutationid, but there is still confusion.