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Error in parsing #70

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DeepColin opened this issue Mar 24, 2021 · 0 comments
Open

Error in parsing #70

DeepColin opened this issue Mar 24, 2021 · 0 comments

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@DeepColin
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DeepColin commented Mar 24, 2021

when I tried to parse the cmap2020, there were errors as follow:

Traceback (most recent call last):
File "get_gct.py", line 17, in
get_gct()
File "get_gct.py", line 13, in get_gct
goo = cp_p.parse('level5_beta_trt_cp_n720216x12328.gctx',cid=brd_cid)
File "/home/wuxiaolong/.conda/envs/my_cmapPy_env/lib/python2.7/site-packages/cmapPy/pandasGEXpress/parse.py", line 68, in parse
make_multiindex=make_multiindex)
File "/home/wuxiaolong/.conda/envs/my_cmapPy_env/lib/python2.7/site-packages/cmapPy/pandasGEXpress/parse_gctx.py", line 110, in parse
data_df = parse_data_df(data_dset, sorted_ridx, sorted_cidx, row_meta, col_meta)
File "/home/wuxiaolong/.conda/envs/my_cmapPy_env/lib/python2.7/site-packages/cmapPy/pandasGEXpress/parse_gctx.py", line 338, in parse_data_df
first_subset = data_dset[cidx, :].astype(np.float32)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1490027549092/work/h5py/_objects.c:2846)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1490027549092/work/h5py/_objects.c:2804)
File "/home/wuxiaolong/.conda/envs/my_cmapPy_env/lib/python2.7/site-packages/h5py/_hl/dataset.py", line 474, in getitem
selection = sel.select(self.shape, args, dsid=self.id)
File "/home/wuxiaolong/.conda/envs/my_cmapPy_env/lib/python2.7/site-packages/h5py/_hl/selections.py", line 90, in select
sel[args]
File "/home/wuxiaolong/.conda/envs/my_cmapPy_env/lib/python2.7/site-packages/h5py/_hl/selections.py", line 392, in getitem
mshape = list(count)
UnboundLocalError: local variable 'count' referenced before assignment

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