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klebgenomics / Kaptive

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Double quotes in Abaum OC database #9

Closed LeahRoberts closed 4 years ago

LeahRoberts commented 4 years ago

Hi team,

Thanks for providing the A baumannii database. I noticed a small typo in the OC database that was causing this error: 

BiopythonParserWarning: The NCBI states double-quote characters like " should be escaped as "" (two double - quotes), but here it was not: 'gtrOC1"'
  BiopythonParserWarning,

I fixed the culprits in the database and it worked OK: 

  /gene="gtrOC1"" <---
  /gene="gtrOC18"
  /gene="gtrOC19a"
  /gene="gtrOC1"" <---
  /gene="gtrOC18"
  /gene="gtrOC1"" <---
  /gene="gtrOC18"
  /gene="gtrOC19b"
  /gene="gtrOC1"" <---
  /gene="gtrOC18"

Just wanted to let you know 👍

kelwyres commented 4 years ago

Thanks Leah! Will update the master version.