Hi, thanks for you developing this pipeline to detect NUMTs, and it is wonderful!
I have some question in running the pipeline, for example (just one part):
sample 3 /xxx/NUMT/output/NUMTs_and_Breakpoints_detection/sample/sample.mt.disc.sam /xxx/NUMT/output/NUM
Ts_and_Breakpoints_detection/sample/sample.mt.split.sam /xxx/sample.Mdup.realigned.recal.bam chr13 16865058 16866242
Loaded 3217346917 letters in 3366 sequences
Searched 15947 bases in 107 sequences
/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: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
df_nu['pointGroup'] = df_nu.apply(f_nu, axis=1)
Traceback (most recent call last):
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2898, in get_loc
return self._engine.get_loc(casted_key)
File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1675, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1683, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'pointGroup'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/generic.py", line 3576, in _set_item
loc = self._info_axis.get_loc(key)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2900, in get_loc
raise KeyError(key) from err
KeyError: 'pointGroup'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/xxx/NUMT/searchBreakpoint_fromblatoutputs.py", line 65, in
df_mt['pointGroup'] = df_mt.apply(f_mt, axis=1)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/frame.py", line 3044, in setitem
self._set_item(key, value)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/frame.py", line 3121, in _set_item
NDFrame._set_item(self, key, value)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/generic.py", line 3579, in _set_item
self._mgr.insert(len(self._info_axis), key, value)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/internals/managers.py", line 1198, in insert
block = make_block(values=value, ndim=self.ndim, placement=slice(loc, loc + 1))
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 2744, in make_block
return klass(values, ndim=ndim, placement=placement)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 2400, in init
super().init(values, ndim=ndim, placement=placement)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 131, in init
f"Wrong number of items passed {len(self.values)}, "
ValueError: Wrong number of items passed 22, placement implies 1
And finally I cannot remove the fasta and sam file because they are not exist.
rm: cannot remove /xxx/NUMT/output/NUMTs_and_Breakpoints_detection/sample/sample_chr7.113963386.113965014.fasta': No such file or directory rm: cannot remove/xxx/NUMT/output/NUMTs_and_Breakpoints_detection/sample/sample_chr7.113963386.113965014.sam': No such file or directory
Could you help me to resolve this problem?
Thank you in advance.
Hi, thanks for you developing this pipeline to detect NUMTs, and it is wonderful! I have some question in running the pipeline, for example (just one part):
sample 3 /xxx/NUMT/output/NUMTs_and_Breakpoints_detection/sample/sample.mt.disc.sam /xxx/NUMT/output/NUM Ts_and_Breakpoints_detection/sample/sample.mt.split.sam /xxx/sample.Mdup.realigned.recal.bam chr13 16865058 16866242 Loaded 3217346917 letters in 3366 sequences Searched 15947 bases in 107 sequences /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: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy df_nu['pointGroup'] = df_nu.apply(f_nu, axis=1) Traceback (most recent call last): File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2898, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1675, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1683, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pointGroup'
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/generic.py", line 3576, in _set_item loc = self._info_axis.get_loc(key) File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2900, in get_loc raise KeyError(key) from err KeyError: 'pointGroup'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/xxx/NUMT/searchBreakpoint_fromblatoutputs.py", line 65, in
df_mt['pointGroup'] = df_mt.apply(f_mt, axis=1)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/frame.py", line 3044, in setitem
self._set_item(key, value)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/frame.py", line 3121, in _set_item
NDFrame._set_item(self, key, value)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/generic.py", line 3579, in _set_item
self._mgr.insert(len(self._info_axis), key, value)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/internals/managers.py", line 1198, in insert
block = make_block(values=value, ndim=self.ndim, placement=slice(loc, loc + 1))
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 2744, in make_block
return klass(values, ndim=ndim, placement=placement)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 2400, in init
super().init(values, ndim=ndim, placement=placement)
File "/xxx/miniconda3/envs/NUMT/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 131, in init
f"Wrong number of items passed {len(self.values)}, "
ValueError: Wrong number of items passed 22, placement implies 1
And finally I cannot remove the fasta and sam file because they are not exist.
rm: cannot remove
/xxx/NUMT/output/NUMTs_and_Breakpoints_detection/sample/sample_chr7.113963386.113965014.fasta': No such file or directory rm: cannot remove/xxx/NUMT/output/NUMTs_and_Breakpoints_detection/sample/sample_chr7.113963386.113965014.sam': No such file or directoryCould you help me to resolve this problem? Thank you in advance.
Best, Jing.