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Add read depth option to interface

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eugenefischer
2022-09-26 14:25:47 -05:00
parent 60cf6775c2
commit e795b4cdd0
1 changed files with 24 additions and 4 deletions
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28
src/main/java/InteractiveInterface.java
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@@ -250,6 +250,11 @@ public class InteractiveInterface {
String filename = null; String filename = null;
String cellFile = null; String cellFile = null;
String plateFile = null; String plateFile = null;
Boolean simulateReadDepth = false;
//number of times to read each sequence in a well
Integer readDepth = 1;
Double readErrorRate = 0.0;
Double errorCollisionRate = 0.0;
try { try {
String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data "; String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
str = str.concat("\nrequires a cell sample file and a sample plate file."); str = str.concat("\nrequires a cell sample file and a sample plate file.");
@@ -258,6 +263,23 @@ public class InteractiveInterface {
cellFile = sc.next(); cellFile = sc.next();
System.out.print("\nPlease enter name of an existing sample plate file: "); System.out.print("\nPlease enter name of an existing sample plate file: ");
plateFile = sc.next(); plateFile = sc.next();
System.out.println("\nEnable simulation of sequence read depth and sequence read errors? (y/n)");
String ans = sc.next();
Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
Matcher matcher = pattern.matcher(ans);
if(matcher.matches()){
simulateReadDepth = true;
}
if (simulateReadDepth) {
System.out.print("\nPlease enter read depth (the integer number of reads per sequence): ");
readDepth = sc.nextInt();
System.out.print("\nPlease enter probability of a sequence read error (0.0 to 1.0): ");
readErrorRate = sc.nextDouble();
System.out.println("\nPlease enter the probability of read error collision");
System.out.println("(the likelihood that two read errors produce the same spurious sequence)");
System.out.print("(0.0 to 1.0): ");
errorCollisionRate = sc.nextDouble();
}
System.out.println("\nThe graph and occupancy data will be written to a file."); System.out.println("\nThe graph and occupancy data will be written to a file.");
System.out.print("Please enter a name for the output file: "); System.out.print("Please enter a name for the output file: ");
filename = sc.next(); filename = sc.next();
@@ -505,8 +527,7 @@ public class InteractiveInterface {
System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching"); System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output"); System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)"); System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)");
System.out.println("6) Turn " + getOnOff(!BiGpairSEQ.simulateReadDepth()) + " simulation of read depth and sequence read errors"); System.out.println("6) Maximum weight matching algorithm options");
System.out.println("7) Maximum weight matching algorithm options");
System.out.println("0) Return to main menu"); System.out.println("0) Return to main menu");
try { try {
input = sc.nextInt(); input = sc.nextInt();
@@ -516,8 +537,7 @@ public class InteractiveInterface {
case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph()); case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary()); case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML()); case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
case 6 -> BiGpairSEQ.setSimulateReadDepth(!BiGpairSEQ.simulateReadDepth()); case 6 -> algorithmOptions();
case 7 -> algorithmOptions();
case 0 -> backToMain = true; case 0 -> backToMain = true;
default -> System.out.println("Invalid input"); default -> System.out.println("Invalid input");
} }