Open reedacartwright opened 2 years ago
Here's the beginnings of a proposal for replacing trick with yaml. At the top level, there are three+ sections. parts
defines partitions of the root sequence and the root sequence itself. rules
defines evolutionary models. regions
defines sections of tree space with known topology and branch length, tied to a partition, and has an evolutionary model.
reps: 100 # can be overridden on the command line
seed: [1,2,3] # can be overridden on the command line
parts:
- name: exon_1
length: 1000 # ignored because seq is specified
seq: "ACGT"
type: DNA
rules:
-
name: default
subst:
model: k2p
alpha: 1
freqs: [0,2,3,4]
ins:
rate: 0.01
model: powerlaw
alpha: 1.5
max_len: 100
del:
rate: 0.01
type: powerlaw
alpha: 1.5
max_len: 100
regions:
-
tree: "(A:0.1,B:0.1).R;"
rule: default
part: exon_1
A possible list of tasks that need to be completed to polish up the Dawg 2.0 code base in preparation for a paper.
rapidyaml
library for parsing.