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IMP: Do no allow duplicate records in DNAFASTAFormat #220
IMP: Do no allow duplicate records in DNAFASTAFormat #220
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One problem with this is that it treats the entire header line as the ID. I believe that we need to treat everything between the
, if any) as the ID. Characters after the space are part of the record's description field, and are not subject to the ID uniqueness rules.
>
and the first instance of whitespace (@ebolyen, can you please confirm this for me?
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Yep, that is correct.
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Thanks @ebolyen! @Oddant1, now would be a good time to fix the error message on https://github.com/qiime2/q2-types/pull/220/files#diff-c7c5016b403f1d6d2fb45764b58ae9d6R153 to indicate this situation, too (technically the ID doesn't start with
>
, the refline for the record starts with>
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Are they allowed to have a space immediately after the
>
? We don't currently check for that at all.There was a problem hiding this comment.
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I think the most comprehensive resource is here:
http://scikit-bio.org/docs/0.5.5/generated/skbio.io.format.fasta.html#module-skbio.io.format.fasta
Have fun... 🎉
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I guess if they had a space immediately after the
>
their id would start with a space and that would be silly, so I suppose they can't do that. That seems to be what that format definition implies.There was a problem hiding this comment.
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I would probably interpret it as a "null" ID, but in any case, that is almost certainly a formatting error and we should probably avoid accepting it.