fix #333: record tag/tagF values in .trees (fixed as doc bug)

MesserLab · Jul 26, 2023 · 7e9194d · 7e9194d
1 parent 16d4334
commit 7e9194d
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Showing 5 changed files with 35 additions and 16 deletions.
diff --git a/.../Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt b/.../Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt
@@ -16,7 +16,8 @@ initialize() {
 1000 late() {
 	target = sample(p1.genomes, 1);
 	target.addNewDrawnMutation(m3, 10000);
-	sim.outputFull(tempdir() + "slim_" + simID + ".txt");
+	defineConstant("PATH", tempdir() + "slim_" + simID + ".trees");
+	sim.outputFull(PATH);
 }
 1000:100000 late() {
 	if (sim.countOfMutationsOfType(m3) == 0) {
@@ -25,9 +26,7 @@ initialize() {
 			sim.simulationFinished();
 		} else {
 			cat(simID + ": LOST - RESTARTING\n");
-
-			sim.readFromPopulationFile(tempdir() + "slim_" + simID + ".txt");
-			setSeed(rdunif(1, 0, asInteger(2^62) - 1));
+			sim.readFromPopulationFile(PATH);
 		}
 	}
 }
diff --git a/...Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt b/...Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt
@@ -1,6 +1,7 @@
 // Keywords: tree-sequence recording, tree sequence recording, conditional sweep
 
 initialize() {
+	initializeSLiMOptions(keepPedigrees=T);
 	initializeTreeSeq();
 	initializeMutationRate(1e-8);
 	initializeMutationType("m2", 0.5, "g", -0.01, 1.0);  // deleterious
@@ -14,9 +15,16 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1000 late() {
+	// assign tag values to be preserved
+	inds = sortBy(sim.subpopulations.individuals, "pedigreeID");
+	tags = rdunif(size(inds), 0, 100000);
+	inds.tag = tags;
+	metadataDict = Dictionary("tags", tags);
+
 	target = sample(p1.genomes, 1);
 	target.addNewDrawnMutation(m3, 10000);
-	sim.treeSeqOutput(tempdir() + "slim_" + simID + ".trees");
+	defineConstant("PATH", tempdir() + "slim_" + simID + ".trees");
+	sim.treeSeqOutput(PATH, metadata=metadataDict);
 }
 1000:100000 late() {
 	if (sim.countOfMutationsOfType(m3) == 0) {
@@ -26,9 +34,11 @@ initialize() {
 			sim.simulationFinished();
 		} else {
 			cat(simID + ": LOST - RESTARTING\n");
-
-			sim.readFromPopulationFile(tempdir() + "slim_" + simID + ".trees");
-			setSeed(rdunif(1, 0, asInteger(2^62) - 1));
+			sim.readFromPopulationFile(PATH);
+			metadataDict = treeSeqMetadata(PATH);
+			tags = metadataDict.getValue("tags");
+			inds = sortBy(sim.subpopulations.individuals, "pedigreeID");
+			inds.tag = tags;
 		}
 	}
 }
diff --git a/.../Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt b/.../Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt
@@ -16,7 +16,8 @@ initialize() {
 1000 late() {
 	target = sample(p1.genomes, 1);
 	target.addNewDrawnMutation(m3, 10000);
-	sim.outputFull(tempdir() + "slim_" + simID + ".txt");
+	defineConstant("PATH", tempdir() + "slim_" + simID + ".trees");
+	sim.outputFull(PATH);
 }
 1000:100000 late() {
 	if (sim.countOfMutationsOfType(m3) == 0) {
@@ -25,9 +26,7 @@ initialize() {
 			sim.simulationFinished();
 		} else {
 			cat(simID + ": LOST - RESTARTING\n");
-
-			sim.readFromPopulationFile(tempdir() + "slim_" + simID + ".txt");
-			setSeed(rdunif(1, 0, asInteger(2^62) - 1));
+			sim.readFromPopulationFile(PATH);
 		}
 	}
 }
diff --git a/...Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt b/...Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt
@@ -1,6 +1,7 @@
 // Keywords: tree-sequence recording, tree sequence recording, conditional sweep
 
 initialize() {
+	initializeSLiMOptions(keepPedigrees=T);
 	initializeTreeSeq();
 	initializeMutationRate(1e-8);
 	initializeMutationType("m2", 0.5, "g", -0.01, 1.0);  // deleterious
@@ -14,9 +15,16 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1000 late() {
+	// assign tag values to be preserved
+	inds = sortBy(sim.subpopulations.individuals, "pedigreeID");
+	tags = rdunif(size(inds), 0, 100000);
+	inds.tag = tags;
+	metadataDict = Dictionary("tags", tags);
+
 	target = sample(p1.genomes, 1);
 	target.addNewDrawnMutation(m3, 10000);
-	sim.treeSeqOutput(tempdir() + "slim_" + simID + ".trees");
+	defineConstant("PATH", tempdir() + "slim_" + simID + ".trees");
+	sim.treeSeqOutput(PATH, metadata=metadataDict);
 }
 1000:100000 late() {
 	if (sim.countOfMutationsOfType(m3) == 0) {
@@ -26,9 +34,11 @@ initialize() {
 			sim.simulationFinished();
 		} else {
 			cat(simID + ": LOST - RESTARTING\n");
-
-			sim.readFromPopulationFile(tempdir() + "slim_" + simID + ".trees");
-			setSeed(rdunif(1, 0, asInteger(2^62) - 1));
+			sim.readFromPopulationFile(PATH);
+			metadataDict = treeSeqMetadata(PATH);
+			tags = metadataDict.getValue("tags");
+			inds = sortBy(sim.subpopulations.individuals, "pedigreeID");
+			inds.tag = tags;
 		}
 	}
 }
diff --git a/VERSIONS b/VERSIONS
@@ -121,6 +121,7 @@ development head (in the master branch):
 	bug fix in pyslim to announce: https://github.com/tskit-dev/pyslim/issues/307
 	feature request: #378, add font bigger (command +) and font smaller (command -) menu items and shortcuts, so the user doesn't have to open the prefs window; note that with command = the shift key is needed
 		this meant removal of the shortcuts for prettyprint script and reformat script, since they conflicted (well, prettyprint conflicted); probably nobody cares
+	revised recipe 17.3 to show how to persist tag values from a simulation in the tree-sequence metadata
 
 
 version 4.0.1 (Eidos version 3.0.1):