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Rename and update readme

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efischer
2022-02-20 11:58:12 -06:00
parent 74c8cafd81
commit f2b5d9e1b7
7 changed files with 52 additions and 15 deletions
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8
.idea/artifacts/TCellSim_jar.xml → .idea/artifacts/BiGpairSEQ_Sim_jar.xml generated
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@@ -1,11 +1,11 @@
<component name="ArtifactManager">
<artifact type="jar" name="TCellSim:jar">
<output-path>$PROJECT_DIR$/out/artifacts/TCellSim_jar</output-path>
<root id="archive" name="TCellSim.jar">
<artifact type="jar" build-on-make="true" name="BiGpairSEQ_Sim:jar">
<output-path>$PROJECT_DIR$/out/artifacts/BiGpairSEQ_Sim_jar</output-path>
<root id="archive" name="BiGpairSEQ_Sim.jar">
<element id="directory" name="META-INF">
<element id="file-copy" path="$PROJECT_DIR$/src/main/java/META-INF/MANIFEST.MF" />
</element>
<element id="module-output" name="TCellSim" />
<element id="module-output" name="BigPairSEQ" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.5.0/commons-cli-1.5.0.jar" path-in-jar="/" />

2
.idea/compiler.xml generated
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@@ -6,7 +6,7 @@
<sourceOutputDir name="target/generated-sources/annotations" />
<sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
<outputRelativeToContentRoot value="true" />
<module name="TCellSim" />
<module name="BigPairSEQ" />
</profile>
</annotationProcessing>
</component>

BIN
out/artifacts/TCellSim_jar/TCellSim.jar → out/artifacts/BiGpairSEQ_Sim_jar/BiGpairSEQ_Sim.jar
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32
out/artifacts/BiGpairSEQ_Sim_jar/readme.md Normal file
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@@ -0,0 +1,32 @@
BiGpairSEQ SIMULATOR
ABOUT:
This program simulates BiGpairSEQ, a graph theory based adaptation
of the pairSEQ algorithm for pairing T cell receptor sequences.
Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and compares
against a null distribution, BiGpairSEQ does not do any statistical calculations
directly. Instead, BiGpairSEQ creates a simple bipartite weighted graph representing the sample plate.
The distinct TCRA and TCRB sequences form the two sets of vertices. Every TCRA/TCRB pair that share a well
are connected by an edge, with the edge weight set to the number of wells in which both sequences appear.
(Sequences in all wells are filtered out prior to creating the graph, as there is no signal in their occupancy
The problem of pairing TCRA/TCRB sequences thus reduces to the "assignment problem" of finding a maximum weight
matching on a bipartite graph--the subset of vertex-disjoint edges whose weights sum to the maximum possible value.
USAGE
Released as an executable .jar file with interactive, command line UI
Usage: java -jar BiGpairSEQ_Sim.jar
Large cell sample or sample plate files may require large amounts of RAM.
It is often desirable to increase the JVM memory allocation with the -Xmx flag
For example, to run the program with 32 gigabytes of memory, use command:
java -Xmx32G -jar BiGpairSEQ_Sim.jar
Requires Java11 or higher (Openjdk-17 recommended)
pairSEQ citation:
Howie, B., Sherwood, A. M., et. al.
"High-throughput pairing of T cell receptor alpha and beta sequences."
Sci. Transl. Med. 7, 301ra131 (2015)
Simulation by Eugene Fischer, 2021-2022

7
out/artifacts/TCellSim_jar/readme.md
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@@ -1,7 +0,0 @@
Executable .jar file with interactive, command line UI
Usage: java -jar TCellSim.jar
To increase memory allocation, use -Xmx flag.
For example, to give the program 20 gigabytes of memory:
java -Xmx20G -jar TCellSim.jar
Requires Java11 or higher (Openjdk-17 recommended)

1
src/main/java/Plate.java
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@@ -55,6 +55,7 @@ public class Plate {
List<Integer[]> well = new ArrayList<>();
for (int j = 0; j < concentrations[section]; j++) {
do {
//inverse transform sampling: for random number u in [0,1), x = log(1-u) / (-lambda)
m = (Math.log10((1 - rand.nextDouble()))/(-lambda)) * Math.sqrt(cells.size());
} while (m >= cells.size() || m < 0);
n = (int) Math.floor(m);

17
src/main/java/UserInterface.java
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@@ -269,7 +269,7 @@ public class UserInterface {
//Need to re-do the CDR3/CDR1 matching to correspond to new pattern
//System.out.println("5) Generate CDR3/CDR1 occupancy graph");
//System.out.println("6) Simulate CDR3/CDR1 T cell matching");
System.out.println("9) Acknowledgements");
System.out.println("9) About/Acknowledgments");
System.out.println("0) Exit");
try {
input = sc.nextInt();
@@ -384,8 +384,8 @@ public class UserInterface {
System.out.println("1) Poisson");
System.out.println("2) Gaussian");
System.out.println("3) Exponential");
System.out.println("(Note: approximate distribution in original paper is exponential, lambda = 0.6.)");
System.out.println("(approximated from slope of log-log graph in figure 4c)");
System.out.println("(Note: approximate distribution in original paper is exponential, lambda = 0.6)");
System.out.println("(lambda value approximated from slope of log-log graph in figure 4c)");
System.out.println("(Note: wider distributions are more memory intensive to match)");
System.out.print("Enter selection value: ");
input = sc.nextInt();
@@ -664,6 +664,17 @@ public class UserInterface {
System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");
System.out.println("");
System.out.println("Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and compares");
System.out.println("against a null distribution, BiGpairSEQ does not do any statistical calculations");
System.out.println("directly. Instead, BiGpairSEQ creates a simple bipartite weighted graph representing");
System.out.println("the sample plate. The distinct TCRA and TCRB sequences form the two sets of vertices.");
System.out.println("Every TCRA/TCRB pair that share a well are connected by an edge, with the edge weight");
System.out.println("set to the number of wells in which both sequences appear. (Sequences in all wells are");
System.out.println("filtered out prior to creating the graph, as there is no signal in their occupancy");
System.out.println("pattern.) The problem of pairing TCRA/TCRB sequences thus reduces to the \"assignment");
System.out.println("problem\" of finding a maximum weight matching on a bipartite graph--the subset of");
System.out.println("vertex-disjoint edges whose weights sum to the maximum possible value.");
System.out.println("");
System.out.println("pairSEQ citation:");
System.out.println("Howie, B., Sherwood, A. M., et. al.");
System.out.println("High-throughput pairing of T cell receptor alpha and beta sequences.");