How to calculate immune diversity?

[To be updated for ImReP output]

Based on IgBLAST result one can quantify immune response based on the combinatorial diversity of BCR and TCR loci. We consider reads spanning V(D)J recombinations and estimate the relative proportion of each recombination. Per sample immune diversity is estimated measured using the alpha diversity (measured by Shannon entropy) and incorporates total number of V(D)J combinations and their relative proportions.

Please use /rop/source/diversity/alphaGeneral.py to calculate the total number of reads spanning the V(D)J recombinations, number of V(D)J recombinations and alpha diversity measured by Shannon entropy for all the samples in 'raw/VJ_recombination/IGK_VJ/' directory. The results are saved into alphaIGK_VJ.csv located in alpha directory. Make sure to provide the extension of the files.

python <ropDir>/rop/source/diversity/alphaGeneral.py raw/VJ_recombination/IGK_VJ/ alpha IGK_VJ 0 1 IGK_igblast.IGK_recomb