KeyError: 'chr' about methplotlib HOT 3 CLOSED

Hi,

That makes no sense at all to me :) Would it be possible to confirm that the problem is still there with version 0.21.0?
I haven't been spending much time on methplotlib recently, but I hope to change that soon.

Wouter

from methplotlib.

Dear Wouter,
Thanks so much for answers me back. the problem got fix adding the bed file to the test script.
Nonetheless, I am having another error when I do try to run call and frequencies on the script as you suggested on the test script:
methplotlib -m ACTB_calls.tsv meth_freq.tsv
-n calls frequencies
-w chr7:5,525,542-5,543,028
-g g38-locus.gtf
-b DNase_cluster.bed
--simplify \

I have this error:

_**Traceback (most recent call last):
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3621, in get_loc
return self._engine.get_loc(casted_key)
File "pandas/_libs/index.pyx", line 136, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 142, in pandas._libs.index.IndexEngine.get_loc
TypeError: '51 False
84 False
193 False
244 False
376 False
...
12160 True
12218 False
12328 True
12430 True
12473 True
Name: log_lik_ratio, Length: 25502, dtype: bool' is an invalid key

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/series.py", line 1085, in setitem
self._set_with_engine(key, value)
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/series.py", line 1146, in _set_with_engine
loc = self.index.get_loc(key)
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3628, in get_loc
self._check_indexing_error(key)
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 5637, in _check_indexing_error
raise InvalidIndexError(key)
pandas.errors.InvalidIndexError: 51 False
84 False
193 False
244 False
376 False
...
12160 True
12218 False
12328 True
12430 True
12473 True
Name: log_lik_ratio, Length: 25502, dtype: bool

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Applic.HPC/Easybuild/skylake/2022a/software/methplotlib/0.20.1-foss-2022a/bin/methplotlib", line 8, in
sys.exit(main())
File "/Applic.HPC/Easybuild/skylake/2022a/software/methplotlib/0.20.1-foss-2022a/lib/python3.10/site-packages/methplotlib/methplotlib.py", line 26, in main
meth_browser(meth_data=meth_data,
File "/Applic.HPC/Easybuild/skylake/2022a/software/methplotlib/0.20.1-foss-2022a/lib/python3.10/site-packages/methplotlib/methplotlib.py", line 53, in meth_browser
meth_traces = plots.methylation(meth_data, dotsize=dotsize, binary=binary, minqual=minqual)
File "/Applic.HPC/Easybuild/skylake/2022a/software/methplotlib/0.20.1-foss-2022a/lib/python3.10/site-packages/methplotlib/plots.py", line 106, in methylation
make_per_read_meth_traces_llr(table=meth.table,
File "/Applic.HPC/Easybuild/skylake/2022a/software/methplotlib/0.20.1-foss-2022a/lib/python3.10/site-packages/methplotlib/plots.py", line 183, in make_per_read_meth_traces_llr
table.loc[:, "llr_scaled"] = rescale_log_likelihood_ratio(table["log_lik_ratio"].copy())
File "/Applic.HPC/Easybuild/skylake/2022a/software/methplotlib/0.20.1-foss-2022a/lib/python3.10/site-packages/methplotlib/plots.py", line 269, in rescale_log_likelihood_ratio
llr[llr > 0] = scaler.fit_transform(llr[llr > 0].values.reshape(-1, 1)).tolist()
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/series.py", line 1127, in setitem
self._set_values(indexer, value)
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/series.py", line 1185, in _set_values
self._mgr = self.mgr.setitem(indexer=key, value=value)
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/internals/managers.py", line 337, in setitem
return self.apply("setitem", indexer=indexer, value=value)
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/internals/managers.py", line 304, in apply
applied = getattr(b, f)(kwargs)
File "/Applic.HPC/Easybuild/skylake/2022a/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/pandas/core/internals/blocks.py", line 957, in setitem
values[indexer] = value
ValueError: shape mismatch: value array of shape (9792,1) could not be broadcast to indexing result of shape (9792,) "

Sorry to keep bothering you but I really want to use your software to plot my methylation data.

Best,

Tania

from methplotlib.

Dear Wouter,
I fix the problem adding --binary to the script.
Best,

Tania

from methplotlib.