#405 Add PEFF support to tide-index

[William S Noble]

From Jimmy Eng:

"FYI, I've been working to implement support for the PSI's enhanced fasta format (PEFF, http://www.psidev.info/node/363) that encapsulates both amino acid substitutions and variable modifications in the description line of the sequence entries.

X!Tandem has been able to do something like this for years now, I believe using modifications encoded in some ENSEMBL file. More recently a group modified the Morpheus search engine (http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00599) to search the UniProt XML file as the sequence database, allowing it to do the same type of thing with annotated modifications in that format.

PEFF has been in development for over a year now; I'm not sure if they've settled on the exact syntax/format their going to use. I just finished the modification support today although I'm sure a million bugs will pop up when it gets tested. And I'm going to now go work on adding support for the amino acid substitutions which adds its own little set of complexities to work around."