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IMP: Do no allow duplicate records in DNAFASTAFormat #220

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merged 4 commits into from
Aug 21, 2019
Merged

IMP: Do no allow duplicate records in DNAFASTAFormat #220

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IMP: Do no allow duplicate records in DNAFASTAFormat
Oddant1 Jul 18, 2019
ef649e2
SQUASH: Addressing @thermokarst's review
Oddant1 Aug 8, 2019
a9d0a39
SQUASH: Addressing @thermokarst's review
Oddant1 Aug 8, 2019
1744618
SQUASH: Addressing @ebolyen's review
Oddant1 Aug 16, 2019
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6 changes: 6 additions & 0 deletions q2_types/feature_data/_format.py
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Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,7 @@ class DNAFASTAFormat(model.TextFileFormat):
def _validate_lines(self, max_lines):
FASTADNAValidator = re.compile(r'[ACGTURYKMSWBDHVN]+\r?\n?')
last_line_was_ID = False
ids = set()
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with open(str(self), 'rb') as fh:
try:
Expand All @@ -161,6 +162,11 @@ def _validate_lines(self, max_lines):
raise ValidationError('Multiple consecutive IDs '
'starting on line '
f'{line_number-1!r}')
if line in ids:
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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 > and the first instance of whitespace ( , 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.

@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.

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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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@Oddant1 Oddant1 Aug 8, 2019 •
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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.

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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.

raise ValidationError(f'Id on line {line_number} '
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'is a duplicate of another '
'id.')
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ids.add(line)
last_line_was_ID = True
elif re.fullmatch(FASTADNAValidator, line):
last_line_was_ID = False
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