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fhalab / evSeq

Computational tools for extremely low-cost, massively parallel amplicon-based sequencing of every variant in protein mutant libraries.
https://fhalab.github.io/evSeq/
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AaIndStart in RefSeq file cannot tolerate negative values #21

Closed NJPorter closed 3 years ago

NJPorter commented 3 years ago

When trying to analyze a tile in which the variable fragment starts immediately after the start ATG, a problem arises because the "AaIndStart" field of the RefSeqs.csv file cannot tolerate a negative value to allow amino acid indexing to match up with the annotated sequence.

palmhjell commented 3 years ago

I think that once we update the indexing to match the variable region (which is now an input with commit 0ec8dee), it should make this just not ever be an issue, so that we don't have to tolerate negative values at all.

palmhjell commented 3 years ago

Okay, this should now be fixed in 9f0c59b. Negative values are still not tolerated as user inputs, but these indexing values are now specified relative to the end of the forward primer/beginning of the variable region, so I don't currently expect users to need to have negative values.

Negative values are actually totally fine as far as the code goes, so if this is ever still a problem we can just remove the error and allow negative values. But for now I think that situation is outside the use cases for evSeq...

Closing for now.