- changed status to resolved
ValueError when loading non-npz counts file with load_counts()
Issue #56
resolved
lib5c.parsers.counts.load_counts()
first tries to load the countsfile as an NPZ via counts = dict(np.load(countsfile))
and watches for IOError, which we expecte to be thrown when the countsfile is actually a plain text countsfile
we haven't been able to pin this down, but potentially due to changes in numpy it is possible to get
Failed example:
counts = load_counts('test/test.counts', primermap)['Sox2']
Exception raised:
Traceback (most recent call last):
File "...\doctest.py", line 1315, in __run
compileflags, 1) in test.globs
File "<doctest lib5c.plotters.extendable.extendable_heatmap.ExtendableHeatmap[9]>", line 1, in <module>
counts = load_counts('test/test.counts', primermap)['Sox2']
File "...\lib5c\parsers\counts.py", line 249, in load_counts
counts = dict(np.load(countsfile))
File "...\site-packages\numpy\lib\npyio.py", line 451, in load
raise ValueError("Cannot load file containing pickled data "
ValueError: Cannot load file containing pickled data when allow_pickle=False
where instead of an IOError a ValueError is thrown and does not get caught by our except block
one solution could be to catch either ValueError or IOError here
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added changelog, first wave of heatmap speed improvements
closes
#28, closes#47, fixes#56updated flake8 config, simplified .gitignore
→ <<cset af833d51b475>>