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The-Sequence-Ontology / Specifications

GFF and GVF specification documents
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'@' Variant_seq option defined in introduction but not in Variant_seq definition section #4

Open thefferon opened 8 years ago

thefferon commented 8 years ago

From the introductory material, "A Quick Explanation and Example of GVF Content", under "attributes:Variant_seq":

@ (at): An alias for the sequence found in the Reference_seq attribute.

Other options include: ., -, ~, !, and ^.

The full 'Variant_seq' section, where this required term is defined, reads:

In addition to the observed nucleic acid sequence, several other characters (.-~@!^) are valid values in the Variant_seq attribute. Use of these characters is described below with examples.

However the '@' option is not defined in the examples along with the other characters.

Possibly related: '@' is not accepted as a valid entry for 'Variant_seq' by the current gvf_validator.pl script.

barrymoore commented 6 years ago

@keilbeck @thefferon I think we can drop support for '@'. I don't think it was ever adopted by either our tools or others. If there is no disagreement I'll remove it.

thefferon commented 6 years ago

No disagreement.