Added models

.tests/sequence_evolution_GTR-Codon.json

@@ -0,0 +1 @@
+{"Contact Network": {"model": "Complete", "param": {"n": 100}}, "Transmission Network": {"model": "Susceptible-Infected-Removed (SIR)", "param": {"N_S": 95, "N_I": 5, "N_R": 0, "R_S-I": 0.0, "R_S-I_I": 2.0, "R_I-R": 1.0, "duration": 10.0}}, "Sample Times": {"model": "State Entry (Initial)", "param": {"sampled_states": "R"}}, "Viral Phylogeny (Seeds)": {"model": "Yule", "param": {"height": 0.1}}, "Viral Phylogeny (Transmissions)": {"model": "Transmission Tree", "param": {}}, "Mutation Rates": {"model": "Constant", "param": {"rate": 5.0}}, "Sequence Evolution": {"model": "General Time-Reversible (GTR) + Codon", "param": {"p_A": 0.25, "p_C": 0.25, "p_G": 0.25, "p_T": 0.25, "r_A-C": 1.0, "r_A-G": 1.0, "r_A-T": 1.0, "r_C-G": 1.0, "r_C-T": 1.0, "r_G-T": 1.0, "r_site1": 2.0, "r_site2": 3.0, "r_site3": 4.0}}, "Ancestral Sequence": {"model": "Exact Base Frequencies", "param": {"k": 100, "p_A": 0.1, "p_C": 0.2, "p_G": 0.3, "p_T": 0.4}}}

global.json

@@ -1370,10 +1370,6 @@
                     "r_site3": {
                         "TYPE": "non-negative float",
                         "DESC": "Relative rate of substitution at codon site 3"
-                    },
-                    "prop_invariable": {
-                        "TYPE": "probability",
-                        "DESC": "Proportion of invariable sites"
                     }
                 },
                 "DESC": "Sequences evolve according to a <ansired>General Time-Reversible (GTR)</ansired>\nsubstitution model with <ansired>codon</ansired>-specific rate heterogeneity."

plugins/sequence_evolution/__init__.py

@@ -3,6 +3,7 @@
 from . import seqgen
 PLUGIN_FUNCTIONS = {
     "General Time-Reversible (GTR)": seqgen.seqgen_gtr,
+    "General Time-Reversible (GTR) + Codon": seqgen.seqgen_gtr_codon,
     "General Time-Reversible (GTR) + Gamma": seqgen.seqgen_gtr_gamma,
     "None": DUMMY_PLUGIN_FUNC,
 }

plugins/sequence_evolution/seqgen.py

@@ -20,18 +20,20 @@ def seqgen(mode, params, out_fn, config, verbose=True):
     seqgen_log_fn = "%s/seqgen.log" % out_fn['intermediate']
     f = open(seqgen_tree_fn, 'w'); f.write("1 %d\nROOT %s\n1\n%s" % (len(root_seq),root_seq,treestr)); f.close()
     command = ['seq-gen', '-of', '-k1']
-    if mode in {'GTR', 'GTR+G'}: # add model
+    if mode in {'GTR', 'GTR+G', 'GTR+Codon'}: # GTR model
         command += ['-m', 'GTR']
-    if mode in {'GTR', 'GTR+G'}: # add base frequencies
+    if mode in {'GTR', 'GTR+G', 'GTR+Codon'}: # add base frequencies
         command += (['-f'] + [str(params['p_%s' % n]) for n in 'ACGT'])
-    if mode in {'GTR', 'GTR+G'}: # add GTR transition rates
+    if mode in {'GTR', 'GTR+G', 'GTR+Codon'}: # add GTR transition rates
         command += (['-r'] + [str(params['r_%s-%s' % tuple(pair)]) for pair in ['AC', 'AG', 'AT', 'CG', 'CT', 'GT']])
     if mode in {'GTR', 'GTR+G'}: # add proportion invariable
         command += ['-i', str(params['prop_invariable'])]
     if mode in {'GTR+G'}: # add Gamma parameters
         command += ['-a', str(params['alpha'])]
         if params['num_cats'] > 0:
             command += ['-g', str(params['num_cats'])]
+    if mode in {'GTR+Codon'}: # add Codon parameters
+        command += ['-c', str(params['r_site1']), str(params['r_site2']), str(params['r_site3'])]
     command += [seqgen_tree_fn]
     if verbose:
         print_log("Command: %s" % ' '.join(command))
@@ -44,5 +46,7 @@ def seqgen(mode, params, out_fn, config, verbose=True):
 # model-specific functions
 def seqgen_gtr(params, out_fn, config, verbose=True):
     seqgen("GTR", params, out_fn, config, verbose=verbose)
+def seqgen_gtr_codon(params, out_fn, config, verbose=True):
+    seqgen("GTR+Codon", params, out_fn, config, verbose=verbose)
 def seqgen_gtr_gamma(params, out_fn, config, verbose=True):
     seqgen("GTR+G", params, out_fn, config, verbose=verbose)