hardingnj / xpclr

Code to compute the XP-CLR statistic to infer natural selection
MIT License
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ValueError: Wrong number of columns at line #76

Open mayufeifei28 opened 2 years ago

mayufeifei28 commented 2 years ago

Hi,

Thanks for this great tool. I have encountered the following error while running it. It works fine in five out of seven chrs. But there is this type of error on two chrs. Any help would be greatly appreciated.

2022-03-04 14:09:27 : INFO : running xpclr v1.1.2 2022-03-04 14:09:27 : INFO : Loading TXT Traceback (most recent call last): File "/opt/main/xpclr/1.1.2/bin/xpclr", line 4, in import('pkg_resources').run_script('xpclr==1.1.2', 'xpclr') File "/opt/main/python/3.9.1/lib/python3.9/site-packages/pkg_resources/init.py", line 665, in run_script self.require(requires)[0].run_script(script_name, ns) File "/opt/main/python/3.9.1/lib/python3.9/site-packages/pkg_resources/init.py", line 1470, in run_script exec(script_code, namespace, namespace) File "/opt/main/xpclr/1.1.2/lib/python3.9/site-packages/xpclr-1.1.2-py3.9.egg/EGG-INFO/scripts/xpclr", line 196, in File "/opt/main/xpclr/1.1.2/lib/python3.9/site-packages/xpclr-1.1.2-py3.9.egg/EGG-INFO/scripts/xpclr", line 130, in main File "/opt/main/xpclr/1.1.2/lib/python3.9/site-packages/xpclr-1.1.2-py3.9.egg/xpclr/util.py", line 82, in load_text_format_data File "/opt/main/python/3.9.1/lib/python3.9/site-packages/numpy/lib/npyio.py", line 1139, in loadtxt for x in read_data(_loadtxt_chunksize): File "/opt/main/python/3.9.1/lib/python3.9/site-packages/numpy/lib/npyio.py", line 1063, in read_data raise ValueError("Wrong number of columns at line %d" ValueError: Wrong number of columns at line 6562062

Thanks,

Yu

hardingnj commented 2 years ago

Hi, Sorry for the slow response on this. Under the hood, this uses the numpy function np.loadtxt. I would suggest double checking that this function can load your text file.

Given the large line number, I might guess that this is infact the last line of your file, and perhaps there is a trailing linebreak? Easily done if you have loaded this file in a text editor.