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Show a warning if special fasta headers format is violated #2

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kim-fehl opened this issue Apr 25, 2021 · 2 comments
Open

Show a warning if special fasta headers format is violated #2

kim-fehl opened this issue Apr 25, 2021 · 2 comments

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@kim-fehl
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In a large dataset of automatically downloaded sequences there can be names including "|" symbol.
I concatenate class and train/test labels also automatically.
So, when I try to analyze this file, there are uninformative error messages like:

  • ValueError: could not convert string to float: 'P42577.2'
  • ValueError: invalid literal for int() with base 10: '6LPD'

which are caused by incorrect fasta headers:

  • P42577.2_sp|P42577.2|FRIS_LYMST|0|training
  • 6LPD_pdb|6LPD|F|1|training

A simple check when importing the file could show a warning to the user.

@Superzchen
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Thank you for your suggestion. We will deal with this problem as soon as possible.

@li6in9muyou
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I added a helpful error message for ill-formed headers in PR #3.

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