FASTA parser should generate unique ids #591

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1. jakebeal commented on May 16, 2019

   

   jakebeal

   on May 16, 2019

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   Shouldn't the IDs be 1T38:A, 1T38:B, and 1T38:C?
2. cjmyers commented on May 17, 2019

   

   cjmyers

   on May 17, 2019

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   Currently the header line is split at ":" with left side being displayId and right side being description. I swear I saw this mentioned somewhere, but I now cannot find it. I did find this interesting blog post about this issue:

   http://www.acgt.me/blog/2013/6/25/the-fasta-file-format-a-showcase-for-the-best-and-worst-of-b.html

   Apparently, the whole line must be unique, but any subset of it is not guaranteed to be unique. Probably the only solution is to take the header line and hash it to try to come up with some sort of unique id.
3. jakebeal commented on May 17, 2019

   

   jakebeal

   on May 17, 2019

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   I think that making a hash is a good way to check if you're dealing with duplicates or not.

   I would strongly suggest staying away from using hashes in names except when forced, however, as that will tend to break the relationship with UIDs used elsewhere. Searching for 1T38, for example, brings up what you'd want to find for these sequences in a whole bunch of databases, so it can't just be delegated to provenance.

   My suggestion:

   1. Record the most common formats (e.g., NCBI) and try parsing with them to see if we can be assured of having the right ID.
   2. Check for duplicates using hashing.
   3. If we don't understand the header and have a conflict, then as a fallback, differentiate with ID-hash[6 char hash]
4. cjmyers

   self-assigned this

   on Jul 11, 2019
5. cjmyers

   added

   change

   on Jul 11, 2019
6. cjmyers

   added this to the SBOL 2.5 milestone on Jul 11, 2019