Mismatching Logic

[gmkarl]

Hey,

I'm confused by a line of logic in the code.

On line 49, the code waits until it picks a set of codons that are found within the last sequence:

SeqSpawnR/R/SequenceSpawner.R

Line 48 in 91d5857

if(RandomCodonSet %>% grep(sequences[x], fixed = TRUE) %>% length > 0){

Then once this check passes, it randomly samples all generated sequences to pick one to replace the sequence in:

SeqSpawnR/R/SequenceSpawner.R

Line 49 in 91d5857

Newseed <- str_replace(sequences[sample(1:x, 1)], RandomCodonSet, ReplacementCodonSet)

This seems to mean that it may not replace anything at all, because it will usually randomly pick a sequence different from the one that matched.

Is this the intended behavior?

[AABoyles]

I tried re-writing this passage once before, and it broke the sequence generation in a way I didn't anticipate or understand. (I didn't write the original logic--I just packaged what was an internal R script in our department.) If you can tweak it such that it continues to generate sequences with the same statistical properties, be my guest!