Idea for enhancements SequenceGenerationVDJ and missing D segment choice for gen_rnd_prod_CDR3 #17
Description
Hello,
I started working on a project where we got TCRB CDR3 sequences of mice that were modified to have down-regulated or completely silenced TdT activity. I wanted to use your package to generate more of these sequences to compare results from actual data to randomly generated sequences.
Unfortunately, it seems it is not possible to generate random productive CDR3 beta sequences without inserted nucleotides from TdT with your current package. I tried to edit the source code locally and added a function to the SequenceGenerationVDJ class that created a sequence in the same way that you did only leaving out the inserted nucleotides, and it works pretty well and didn't take long to implement. I thought I might as well share it here so you might think of adding this as a feature sometime to have more control over the sequences produced. Of course, you could also do the same for SequenceGenerationVJ.
While I did this, I noticed that the gen_rnd_prod_CDR3 function for SequenceGenerationVDJ did not return the choice of D segment used. I assume this is a bug as I'd also like to know which D segment was used.
Cheers,
Gabe van den Hoeven