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When I run cooler cload -c1 1 -p1 2 -c2 4 - p2 5 .. on a file with four columns:
galactic 1601634 galactic 1125339
galactic 1601743 galactic 1135340
galactic 1597121 galactic 1126359
galactic 1598993 galactic 1135185
galactic 1597588 galactic 1125826
The error I get is:
Traceback (most recent call last):
File "/Users/peter/miniconda3/envs/cenv3/bin/cooler", line 11, in <module>
load_entry_point('cooler', 'console_scripts', 'cooler')()
File "/Users/peter/miniconda3/envs/cenv3/lib/python3.6/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/Users/peter/miniconda3/envs/cenv3/lib/python3.6/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/Users/peter/miniconda3/envs/cenv3/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/peter/miniconda3/envs/cenv3/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/peter/miniconda3/envs/cenv3/lib/python3.6/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/peter/miniconda3/envs/cenv3/lib/python3.6/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/Users/peter/projects/cooler.mirnylab/cooler/cli/cload.py", line 409, in pairs
ensure_sorted=False
File "/Users/peter/projects/cooler.mirnylab/cooler/io.py", line 510, in create_from_unordered
create(cool_uri, bins, chunks, columns=columns, dtype=dtype, **kwargs)
File "/Users/peter/projects/cooler.mirnylab/cooler/io.py", line 286, in create
file_path, target, meta.columns, iterable, h5opts, lock)
File "/Users/peter/projects/cooler.mirnylab/cooler/_writer.py", line 203, in write_pixels
for i, chunk in enumerate(iterable):
File "/Users/peter/projects/cooler.mirnylab/cooler/_binning.py", line 701, in __iter__
ignore_index=True)
File "/Users/peter/miniconda3/envs/cenv3/lib/python3.6/site-packages/pandas/tools/merge.py", line 1334, in concat
copy=copy)
File "/Users/peter/miniconda3/envs/cenv3/lib/python3.6/site-packages/pandas/tools/merge.py", line 1367, in __init__
raise ValueError('No objects to concatenate')
ValueError: No objects to concatenate
A much more informative error would be that the column I specified for p2 is invalid since the file only has 4 columns.
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