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sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
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Megares Downloading Error #294

Closed ajkarloss closed 4 years ago

ajkarloss commented 4 years ago

Command used "ariba getref megares Megares.out". Many of my colleagues are also reporting the same.

raise Error('Unexpected header in annotations file. Expected columns: ' + ','.join(expected_columns) + ' but got: ' + ','.join(reader.fieldnames)) ariba.megares_zip_parser.Error: Unexpected header in annotations file. Expected columns: group,class,mechanism,header but got: header,type,class,mechanism,group

puethe commented 4 years ago

Hello @ajkarloss , looks like the new version of megares comes in a different format. We cannot fix that at the moment, as the software is no longer maintained. But you can constrain Ariba to download an older version as e.g. ariba getref megares --version 1.01 Megares.out.

ajkarloss commented 4 years ago

I have modified the code (megares_zip_parser.py) to parse the MEGARes 2.0.0. Shall I send a pull request?

puethe commented 4 years ago

Thanks, but the original developer has just put in his own pull request that will be able to handle both versions 1 and 2. We will take that one.

ajkarloss commented 4 years ago

:) Thanks.