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new plotting for marginal date ranges
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@ktmeaton
ktmeaton committed Apr 2, 2021
1 parent 4b0ea23 commit 954e636
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108 changes: 6 additions & 102 deletions workflow/notebooks/clock_model.py.ipynb
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Expand Up @@ -717,111 +717,15 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"0.00\t-TreeAnc: set-up\n",
"\n",
"0.08\t-SequenceData: loaded alignment.\n",
"0.08\t--SequenceData.aln: specified sequence length doesn't match alignment\n",
" \t length. Treating difference as constant sites.\n",
"\n",
"0.08\t-SeqData: making compressed alignment...\n",
"\n",
"1.55\t-SequenceData: constructed compressed alignment...\n",
"1.62\t--ClockTree: Setting precision to level 2\n",
"\n",
"1.62\t-ClockTree._assign_dates: assigned date contraints to 6 out of 8 tips.\n",
"\n",
"1.62\t-TreeTime._set_branch_length_mode: maximum branch length is 2.721e-05,\n",
" \t using branch length mode joint\n",
"\n",
"1.62\t-TreeAnc.optimize_tree: sequences...\n",
"\n",
"1.62\t-TreeAnc.infer_ancestral_sequences with method: probabilistic, joint\n",
"\n",
"1.62\tWARNING: Previous versions of TreeTime (<0.7.0) RECONSTRUCTED sequences of\n",
" \ttips at positions with AMBIGUOUS bases. This resulted in unexpected\n",
" \tbehavior is some cases and is no longer done by default. If you want to\n",
" \treplace those ambiguous sites with their most likely state, rerun with\n",
" \t`reconstruct_tip_states=True` or `--reconstruct-tip-states`.\n",
"1.62\t--TreeAnc._ml_anc_joint: type of reconstruction: Joint\n",
"1.62\t---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...\n",
"1.64\t---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum\n",
" \t likelihood sequences...\n",
"1.64\t---TreeAnc._ml_anc_joint: ...done\n",
"1.64\t--TreeAnc.infer_gtr: counting mutations...\n",
"1.65\t---TreeAnc.infer_gtr: counting mutations...done\n",
"\n",
"1.65\t-GTR: with alphabet: ['A', 'C', 'G', 'T', '-']\n",
"1.65\t--GTR: ambiguous character: N\n",
"1.65\t---GTR: init with dummy values!\n",
"\n",
"1.65\t-GTR: model inference\n",
"1.65\t---GTR inference iteration 0 change: 0.447213595499958\n",
"1.65\t---GTR inference iteration 1 change: 0.23449022561129462\n",
"1.65\t--The model allows for gaps which are estimated to occur at a low fraction\n",
" \t of 6.788e-05 this can potentially result in artificats. gap fraction will\n",
" \t be set to 0.0100\n",
"1.65\t--TreeAnc.infer_gtr: setting overall rate to 1.0...\n",
"1.66\t--TreeAnc._ml_anc_joint: type of reconstruction: Joint\n",
"1.66\t---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...\n",
"1.67\t---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum\n",
" \t likelihood sequences...\n",
"1.67\t---TreeAnc._ml_anc_joint: ...done\n",
"\n",
"1.67\t-TreeAnc.optimize_branch_length: running branch length optimization using\n",
" \t jointML ancestral sequences\n",
"\n",
"1.75\t-TreeAnc.prune_short_branches: pruning short branches (max prob at zero)...\n",
"\n",
"1.75\t-TreeAnc.infer_ancestral_sequences with method: probabilistic, joint\n",
"1.75\t--TreeAnc._ml_anc_joint: type of reconstruction: Joint\n",
"1.76\t---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...\n",
"1.77\t---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum\n",
" \t likelihood sequences...\n",
"1.77\t---TreeAnc._ml_anc_joint: ...done\n",
"1.77\t--TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev\n",
" \t reconstructions: 0\n",
"1.77\t--TreeAnc.optimize_tree: Unconstrained sequence LH:-6459659.661804\n",
"\n",
"1.77\t-TreeAnc.optimize_tree: sequences...\n",
"\n",
"1.77\t-TreeAnc.infer_ancestral_sequences with method: probabilistic, joint\n",
"1.77\t--TreeAnc._ml_anc_joint: type of reconstruction: Joint\n",
"1.77\t---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...\n",
"1.78\t---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum\n",
" \t likelihood sequences...\n",
"1.78\t---TreeAnc._ml_anc_joint: ...done\n",
"\n",
"1.78\t-TreeAnc.optimize_branch_length: running branch length optimization using\n",
" \t jointML ancestral sequences\n",
"\n",
"1.85\t-TreeAnc.infer_ancestral_sequences with method: probabilistic, joint\n",
"1.85\t--TreeAnc._ml_anc_joint: type of reconstruction: Joint\n",
"1.85\t---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...\n",
"1.86\t---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum\n",
" \t likelihood sequences...\n",
"1.86\t---TreeAnc._ml_anc_joint: ...done\n",
"1.87\t--TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev\n",
" \t reconstructions: 0\n",
"1.87\t--TreeAnc.optimize_tree: Unconstrained sequence LH:-6459659.661804\n",
"\n",
"1.87\t###TreeTime.run: INITIAL ROUND\n",
"\n",
"1.87\t-ClockTree: Maximum likelihood tree optimization with temporal constraints\n",
"1.87\t--ClockTree.init_date_constraints...\n",
"1.87\t---ClockTree.init_date_constraints: Initializing branch length\n",
" \t interpolation objects...\n",
"2.20\t--ClockTree.date2dist: Setting new molecular clock. rate=-3.938e-09,\n",
" \t R^2=0.7392\n",
"2.20\t--ClockTree - Joint reconstruction: Propagating leaves -> root...\n",
"2.80\t--ClockTree - Joint reconstruction: Propagating root -> leaves...\n"
"ename": "SyntaxError",
"evalue": "EOL while scanning string literal (<ipython-input-1-76bfac0e4a9c>, line 19)",
"output_type": "error",
"traceback": [
"\u001b[0;36m File \u001b[0;32m\"<ipython-input-1-76bfac0e4a9c>\"\u001b[0;36m, line \u001b[0;32m19\u001b[0m\n\u001b[0;31m \"tt.run(\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m EOL while scanning string literal\n"
]
}
],
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