search

shahab-sarmashghi / RESPECT

Estimating repeat spectra and genome length from low-coverage genome skims
Other
11 stars 1 forks source link

with the hist file input,I got a IndexError #7

Closed helan-1997 closed 2 years ago

helan-1997 commented 2 years ago

the code I used is as follows: respect -i Unknown_AL483-01R0001-01-R00_good_10w.hist -I hist-info.txt IndexError: single positional indexer is out-of-bounds

shahab-sarmashghi commented 2 years ago

Is hist-info.txt formatted as described in the documentation? See example.

If both .hist and info file have the right format and you still get an error, try to run the command with --debug option and paste the error here please.

helan-1997 commented 2 years ago

yes,there is a problem with the info format.then I still run this code: respect -i Unknown_AL483-01R0001-01-R00_good_10w.hist -I hist-info.txt then: /home/user/miniconda3/envs/respect_env/lib/python3.10/site-packages/respect-1.3.0-py3.10.egg/respect/optimizer.py:234: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self._parameters_dataframe = self._parameters_dataframe.append( /home/user/miniconda3/envs/respect_env/lib/python3.10/site-packages/respect-1.3.0-py3.10.egg/respect/optimizer.py:241: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self._spectra_dataframe = self._spectra_dataframe.append(pd.Series([iteration] + list(self.repeat_spectra), keep circulating.

shahab-sarmashghi commented 2 years ago

These are warnings that you can ignore. Do you still get an error (other than these warnings)?

helan-1997 commented 2 years ago

No problem, thank you.