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buske / silva

SilVA: Silent Variant Analysis using random forests
GNU General Public License v3.0
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ValueError: invalid literal for int() with base 10: '18080854\xc2\xa0' #8

Closed martielafreitas closed 3 years ago

martielafreitas commented 3 years ago

This is the first time I faced an error with SilVA. Anyone to help me?

`Saving genes to pickled file: /home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/data/refGene.pkl Traceback (most recent call last):

File "/home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/src/input/synonymous.py", line 843, in sys.exit(main())

File "/home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/src/input/synonymous.py", line 840, in main script(*args, **kwargs)

File "/home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/src/input/synonymous.py", line 699, in script filter_variants(genes, filename, protein_coords=protein_coords)

File "/home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/src/input/synonymous.py", line 635, in filter_variants pos = int(pos)

ValueError: invalid literal for int() with base 10: '18080854\xc2\xa0' `

buske commented 3 years ago

Hi @martielafreitas, it looks like your input file has a non-breaking space (utf-8 literal: \xc2\xa0) after the position (18080854) on that line. The columns in the input file should be separated by tabs.

martielafreitas commented 3 years ago

True! I have a nbsp at the end of one of my lines. Thanks a lot!