expand valid inputs - Githubissues

Townsend-Lab-Yale / massprf-pipeline

pipeline for genome wide MASSPRF analysis

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expand valid inputs #4

Closed stanleyjs closed 7 years ago

stanleyjs commented 7 years ago

Currently supports small subset of possible inputs:

SNP list (see ellison 2011)
GFF annotation of polymorph references
pre separated FASTA of CDS from divergence
FASTA of polymorph assembly

need to accept:

pre-spliced polymorphs
multiple divergent sequences
unspliced divergent sequences
GFF splicing of odd names (biopython can help here)

stanleyjs commented 7 years ago

@JeffreyTownsend Do you have any suggestions for other inputs to be accepted? I am not sure of all of the possible combinations of inputs that exist

JeffreyTownsend commented 7 years ago

I would just go for the inputs that you see coming in from the data set you are analyzing, for now. We should be able to expand inputs later if and when needed.