We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
There was an error while loading. Please reload this page.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-30-bec833fbac57> in <module>() 2 sample_indices = tuple(sorted(df_samples[df_samples.population == pop].index.values)) 3 for chrom in chromosomes: ----> 4 results_by_pop[pop][chrom] = targets_accumulating_variation(chrom, sample_indices) <ipython-input-15-8f3c421e63a5> in targets_accumulating_variation(chrom, sample_indices) 11 sample_indices = random.sample(sample_indices, len(sample_indices)) 12 for i, sidx in enumerate(sample_indices): ---> 13 is_variant |= get_is_variant(chrom, sidx) 14 loc = base_loc & get_target_is_conserved(is_variant) 15 n_targets = np.count_nonzero(loc) <ipython-input-13-dd88d658f1a4> in get_is_variant(chrom, sample_idx) 4 out = np.zeros_like(seq, dtype=bool) 5 pos = callset_pass[chrom]['variants/POS'][:] ----> 6 g = callset_pass[chrom]['calldata/genotype'][:, sample_idx] 7 loc = np.any(g > 0, axis=1) 8 idx = pos[loc] - 1 /home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/zarr/core.py in __getitem__(self, item) 446 447 # normalize selection --> 448 selection = normalize_array_selection(item, self._shape) 449 450 # determine output array shape /home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/zarr/util.py in normalize_array_selection(item, shape) 184 # determine start and stop indices for all axes 185 selection = tuple(normalize_axis_selection(i, l) --> 186 for i, l in zip(item, shape)) 187 188 # fill out selection if not completely specified /home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/zarr/util.py in <genexpr>(.0) 184 # determine start and stop indices for all axes 185 selection = tuple(normalize_axis_selection(i, l) --> 186 for i, l in zip(item, shape)) 187 188 # fill out selection if not completely specified /home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/zarr/util.py in normalize_axis_selection(item, l) 163 164 else: --> 165 raise TypeError('expected integer or slice, found: %r' % item) 166 167 TypeError: expected integer or slice, found: 736
The text was updated successfully, but these errors were encountered:
test and fix for #143 index with numpy integer item
1c35fa7
df8dbbc
366ed0e
Merge pull request #147 from alimanfoo/issue_143
fa32f1e
Test and fix for #143 index with numpy integer item
No branches or pull requests
The text was updated successfully, but these errors were encountered: