import pyranges as pr
chr_gr = pr.PyRanges(
chromosomes = "chr2",
starts = [0],
ends = [1]
)
chr_gr.to_bigwig("test.bw",
{"chr2":10})
With dependencies:
dependencies = [
"pybigwig>=0.3.25",
"pyranges>=0.1.4",
"pyrle>=0.0.43",
]
Yields the following error:
Traceback (most recent call last):
File "test_bw.py", line 9, in <module>
chr_gr.to_bigwig("test.bw",
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/pyranges/pyranges_main.py", line 5505, in to_bigwig
result = _to_bigwig(self, path, chromosome_sizes, rpm, divide, value_col, dryrun)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/pyranges/out.py", line 199, in _to_bigwig
gr = self.to_rle(rpm=rpm, strand=False, value_col=value_col).to_ranges()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/pyranges/pyranges_main.py", line 5880, in to_rle
return _to_rle(self, value_col, strand=strand, rpm=rpm, nb_cpu=nb_cpu)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/pyranges/methods/to_rle.py", line 18, in _to_rle
result = pyrange_apply_single(coverage, ranges, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/pyranges/multithreaded.py", line 342, in pyrange_apply_single
result = call_f_single(function, nparams, df, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/pyranges/multithreaded.py", line 28, in call_f_single
return f.remote(df, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/pyrle/methods.py", line 156, in coverage
runs, values = _coverage(_df.Position.values, _df.Value.values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pyrle/src/coverage.pyx", line 28, in pyrle.src.coverage._coverage
File "<stringsource>", line 664, in View.MemoryView.memoryview_cwrapper
File "<stringsource>", line 352, in View.MemoryView.memoryview.__cinit__
ValueError: buffer source array is read-onlyTried playing around w/ different versions of pyrle and pybigwig but no luck so far.
With dependencies:
Yields the following error:
Tried playing around w/ different versions of pyrle and pybigwig but no luck so far.