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WeiWei060512 / NUMTs-detection

Detecting NUMTs from WGS
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ValueError: Shape of passed values is (7, 1), indices imply (7, 0) #12

Open jingydz opened 6 months ago

jingydz commented 6 months ago

Hi, I encountered different error when I detected NUMT in different samples.

for example:

538A 2 /shared/home/xxx/xxx/NUMT/output/NUMTs_and_Breakpoints_detection/538A/538A.mt.disc.sam /shared/home/xxx/xxx/NUMT/output/NUMTs_and_Breakpoints_detection/538A/538A.mt.split.s am /shared/home/xxx/xxx/all-samples-Mdup.realigned.recal.bam/538A/538A.Mdup.realigned.recal.bam chr12 7453293 7454607 Loaded 3217346917 letters in 3366 sequences Searched 2576 bases in 18 sequences /shared/home/xxx/xxx/NUMT/searchBreakpoint_fromblatoutputs.py:64: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy df_nu['pointGroup'] = df_nu.apply(f_nu, axis=1) /shared/home/xxx/xxx/NUMT/searchBreakpoint_fromblatoutputs.py:65: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy df_mt['pointGroup'] = df_mt.apply(f_mt, axis=1) /shared/home/xxx/xxx/NUMT/searchBreakpoint_fromblatoutputs.py:66: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy df_nu['chr'] = CHR /shared/home/xxx/xxx/NUMT/searchBreakpoint_fromblatoutputs.py:67: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy df_nu['Group'] = df_nu['pointGroup'].str.replace(r'_T.*B','') /shared/home/xxx/xxx/NUMT/searchBreakpoint_fromblatoutputs.py:68: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy df_mt['chr'] = 'chrM' Traceback (most recent call last): File "/shared/home/xxx/xxx/NUMT/searchBreakpoint_fromblatoutputs.py", line 107, in df_mtConfG = pd.concat([df_mtLeftTstartG,df_mtLeftTendG,df_mtRightTstartG,df_mtRightTendG]) File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/reshape/concat.py", line 213, in concat return op.get_result() File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/reshape/concat.py", line 408, in get_result copy=self.copy) File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/internals.py", line 5202, in concatenate_block_managers return BlockManager(blocks, axes) File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/internals.py", line 3028, in init self._verify_integrity() File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/internals.py", line 3239, in _verify_integrity construction_error(tot_items, block.shape[1:], self.axes) File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/internals.py", line 4603, in construction_error passed, implied)) ValueError: Shape of passed values is (7, 1), indices imply (7, 0)