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pirl-unc / mhcgnomes

Parsing MHC nomenclature in the wild
Apache License 2.0
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lots of debug output #15

Closed timodonnell closed 2 years ago

timodonnell commented 2 years ago

I'm seeing tons of lines like this from mhcflurry.common.normalize_allele_name - I think it is coming from mhcgnomes.parse:

TokenizationResult(tokens=(Token(seq='mafa-i*01:03', raw_string='Mafa-I*01:03'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*01:03, trimmed_string=Mafa-I*01:03)
TokenizationResult(tokens=(Token(seq='mafa-i*01:04', raw_string='Mafa-I*01:04'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*01:04, trimmed_string=Mafa-I*01:04)
TokenizationResult(tokens=(Token(seq='mafa-i*01:05', raw_string='Mafa-I*01:05'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*01:05, trimmed_string=Mafa-I*01:05)
TokenizationResult(tokens=(Token(seq='mafa-i*01:06', raw_string='Mafa-I*01:06'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*01:06, trimmed_string=Mafa-I*01:06)
TokenizationResult(tokens=(Token(seq='mafa-i*01:07', raw_string='Mafa-I*01:07'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*01:07, trimmed_string=Mafa-I*01:07)
TokenizationResult(tokens=(Token(seq='mafa-i*01:08', raw_string='Mafa-I*01:08'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*01:08, trimmed_string=Mafa-I*01:08)
TokenizationResult(tokens=(Token(seq='mafa-i*01:09', raw_string='Mafa-I*01:09'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*01:09, trimmed_string=Mafa-I*01:09)
TokenizationResult(tokens=(Token(seq='mamu-i*01:02', raw_string='Mamu-I*01:02'),), ignored_tokens=(), attributes={}, raw_string=Mamu-I*01:02, trimmed_string=Mamu-I*01:02)
TokenizationResult(tokens=(Token(seq='mafa-i*01:10', raw_string='Mafa-I*01:10'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*01:10, trimmed_string=Mafa-I*01:10)
TokenizationResult(tokens=(Token(seq='mafa-i*03:01', raw_string='Mafa-I*03:01'),), ignored_tokens=(), attributes={}, raw_string=Mafa-I*03:01, trimmed_string=Mafa-I*03:01)
timodonnell commented 2 years ago

I'd submit a PR with the fix deleting that line but need access to this repo

timodonnell commented 2 years ago

Put in PR #16 from a fork of the repo