AttributeError: module 'numpy' has no attribute 'object' in index_summary(run_metrics, level='Barcode')
hotsoupisgood opened this issue · 2 comments
hotsoupisgood commented
Hi I am getting what seems to be an error with how you call np.object in your code.
My code:
from datetime import datetime
from interop import py_interop_run_metrics, py_interop_run, py_interop_summary, index_summary
import json, os
import numpy as np
run = '/path/to/run/dir'
run_metrics = py_interop_run_metrics.run_metrics()
print("Reading run")
run_metrics.read(run)
summary = py_interop_summary.run_summary()
print("Summarizing metrics")
py_interop_summary.summarize_run_metrics(run_metrics, summary)
lanes = summary.lane_count()
index_summary(run_metrics, level='Barcode')
And the error:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[6], line 16
14 py_interop_summary.summarize_run_metrics(run_metrics, summary)
15 lanes = summary.lane_count()
---> 16 index_summary(run_metrics, level='Barcode')
File ~/Library/Python/3.8/lib/python/site-packages/interop/core.py:184, in index_summary(run_metrics, level, columns, dtype, **extra)
182 return np.asarray([])
183 _str_types = ('Index1', 'Index2', 'Sample Id', 'Project Name')
--> 184 return np.asarray(data, dtype=extra_cols+[(col, dtype if col not in _str_types else np.object) for col in header])
File ~/Library/Python/3.8/lib/python/site-packages/interop/core.py:184, in <listcomp>(.0)
182 return np.asarray([])
183 _str_types = ('Index1', 'Index2', 'Sample Id', 'Project Name')
--> 184 return np.asarray(data, dtype=extra_cols+[(col, dtype if col not in _str_types else np.object) for col in header])
File ~/Library/Python/3.8/lib/python/site-packages/numpy/__init__.py:284, in __getattr__(attr)
281 from .testing import Tester
282 return Tester
--> 284 raise AttributeError("module {!r} has no attribute "
285 "{!r}".format(__name__, attr))
AttributeError: module 'numpy' has no attribute 'object'
hotsoupisgood commented
When changed to np.object_ it works again
ezralanglois commented
thanks for the bug report, looks like this only happens with recent versions of numpy. We will fix this in the next release