Merge pull request #61 from CEGRcode/dev

Merge development Three Color Heatmap and Yeast Genome Converter tools

Author: WilliamKMLai

build.gradle

@@ -9,7 +9,7 @@ apply plugin: 'eclipse'
 
 sourceSets.main.java.srcDirs = ['src']
 mainClassName = "main.ScriptManager"
-version = 'v0.13'
+version = 'v0.13-dev'
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 

src/cli/BAM_Format_Converter/BAMtoBEDCLI.java

@@ -19,6 +19,7 @@
 */
 @Command(name = "bam-to-bed", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.bam_to_bed_description,
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	sortOptions = false,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)

src/cli/BAM_Format_Converter/BAMtoGFFCLI.java

@@ -19,6 +19,7 @@
 */
 @Command(name = "bam-to-gff", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.bam_to_gff_description,
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	sortOptions = false,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)

src/cli/BAM_Format_Converter/BAMtobedGraphCLI.java

@@ -19,6 +19,7 @@
 */
 @Command(name = "bam-to-bedgraph", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.bam_to_bedgraph_description,
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	sortOptions = false,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)

src/cli/BAM_Format_Converter/BAMtoscIDXCLI.java

@@ -19,6 +19,7 @@
 */
 @Command(name = "bam-to-scidx", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.bam_to_scidx_description,
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	sortOptions = false,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)

src/cli/BAM_Manipulation/BAIIndexerCLI.java

@@ -13,6 +13,7 @@
 	description = ToolDescriptions.bam_indexer_description + "\n"+
 		"@|bold **Please run the samtools tool directly:**|@ \n"+
 		"@|bold,yellow 'samtools index <bam-file>'|@",
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)
 public class BAIIndexerCLI implements Callable<Integer> {

src/cli/BAM_Manipulation/BAMRemoveDupCLI.java

@@ -14,6 +14,7 @@
 		"@|bold **Please run the picard/samtools tools directly:**|@ \n"+
 		"@|bold,yellow 'java -jar picard.jar MarkDuplicates I=<in.bam> O=<marked.bam>\n"+
 		"samtools view -F 1024 <marked.bam> > <out.bam>'|@",
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)
 public class BAMRemoveDupCLI implements Callable<Integer> {

src/cli/BAM_Manipulation/FilterforPIPseqCLI.java

@@ -11,108 +11,122 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import objects.CustomExceptions.FASTAException;
 import objects.ToolDescriptions;
 import util.FASTAUtilities;
 import util.ExtensionFileFilter;
 import scripts.BAM_Manipulation.FilterforPIPseq;
 
 /**
-	BAM_ManipulatioCLIn/FilterforPIPseqCLI
-*/
-@Command(name = "filter-pip-seq", mixinStandardHelpOptions = true,
-	description = ToolDescriptions.filter_pip_seq_description + "\n" +
-				"Note this program does not index the resulting BAM file and user must use appropriate samtools command to generate BAI.",
-	sortOptions = false,
-	exitCodeOnInvalidInput = 1,
-	exitCodeOnExecutionException = 1)
+ * BAM_ManipulatioCLIn/FilterforPIPseqCLI
+ */
+@Command(name = "filter-pip-seq", mixinStandardHelpOptions = true, description = ToolDescriptions.filter_pip_seq_description
+		+ "\n"
+		+ "Note this program does not index the resulting BAM file and user must use appropriate samtools command to generate BAI.", version = "ScriptManager "
+				+ ToolDescriptions.VERSION, sortOptions = false, exitCodeOnInvalidInput = 1, exitCodeOnExecutionException = 1)
 public class FilterforPIPseqCLI implements Callable<Integer> {
-	
-	@Parameters( index = "0", description = "The reference genome FASTA file.")
+
+	@Parameters(index = "0", description = "The reference genome FASTA file.")
 	private File genomeFASTA;
-	@Parameters( index = "1", description = "The BAM file from which we filter.")
+	@Parameters(index = "1", description = "The BAM file from which we filter.")
 	private File bamFile;
-	
-	@Option(names = {"-o", "--output"}, description = "specify output file (default=<bamFileNoExt>_PSfilter.bam)")
+
+	@Option(names = { "-o", "--output" }, description = "specify output file (default=<bamFileNoExt>_PSfilter.bam)")
 	private File output = null;
-	@Option(names = {"-f", "--filter"}, description = "filter by upstream sequence, works only for single-nucleotide A,T,C, or G. (default seq ='T')")
+	@Option(names = { "-f",
+			"--filter" }, description = "filter by upstream sequence, works only for single-nucleotide A,T,C, or G. (default seq ='T')")
 	private String filterString = "T";
-	
+
 	@Override
 	public Integer call() throws Exception {
-		System.err.println( ">FilterforPIPseqCLI.call()" );
+		System.err.println(">FilterforPIPseqCLI.call()");
 		String validate = validateInput();
-		if(!validate.equals("")){
-			System.err.println( validate );
+		if (!validate.equals("")) {
+			System.err.println(validate);
 			System.err.println("Invalid input. Check usage using '-h' or '--help'");
 			System.exit(1);
 		}
-		
-		FilterforPIPseq script_obj = new FilterforPIPseq(bamFile, genomeFASTA, output, filterString, null);
-		script_obj.run();
-		
-		System.err.println( "BAM Generated." );
-		return(0);
+
+		try {
+			FilterforPIPseq script_obj = new FilterforPIPseq(bamFile, genomeFASTA, output, filterString, null);
+			script_obj.run();
+		} catch (FASTAException e) {
+			System.err.println(e.getMessage() + "\n");
+		}
+
+		System.err.println("BAM Generated.");
+		return (0);
 	}
-	
-	//validateInput outline
+
+	// validateInput outline
 	private String validateInput() throws IOException {
 		String r = "";
-		
-		//check inputs exist
-		if(!bamFile.exists()){
+
+		// check inputs exist
+		if (!bamFile.exists()) {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 		}
-		if(!genomeFASTA.exists()){
+		if (!genomeFASTA.exists()) {
 			r += "(!)FASTA file does not exist: " + genomeFASTA.getName() + "\n";
 		}
-		if(!r.equals("")){ return(r); }
-		//check input extensions
+		if (!r.equals("")) {
+			return (r);
+		}
+		// check input extensions
 		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if(!faFilter.accept(genomeFASTA)){
+		if (!faFilter.accept(genomeFASTA)) {
 			r += "(!)Is this a FASTA file? Check extension: " + genomeFASTA.getName() + "\n";
 		}
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
+		if (!"bam".equals(ExtensionFileFilter.getExtension(bamFile))) {
 			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
 		}
-		//check BAI exists
-		File f = new File(bamFile+".bai");
-		if(!f.exists() || f.isDirectory()){
+		// check BAI exists
+		File f = new File(bamFile + ".bai");
+		if (!f.exists() || f.isDirectory()) {
 			r += "(!)BAI Index File does not exist for: " + bamFile.getName() + "\n";
 		}
-		//check FAI exists (generate if not)
+		// check FAI exists (generate if not)
 		File FAI = new File(genomeFASTA + ".fai");
-		if(!FAI.exists() || FAI.isDirectory()) {
+		if (!FAI.exists() || FAI.isDirectory()) {
 			System.err.println("FASTA Index file not found.\nGenerating new one...\n");
-			boolean FASTA_INDEX = FASTAUtilities.buildFASTAIndex(genomeFASTA);
-			if(!FASTA_INDEX){ r += "FASTA Index failed to build."; }
+			try {
+				FASTAUtilities.buildFASTAIndex(genomeFASTA);
+			} catch (FASTAException e) {
+				r += e.getMessage();
+			}
+
 		}
-		//set default output filename
-		if(output==null){
+		// set default output filename
+		if (output == null) {
 			output = new File(ExtensionFileFilter.stripExtension(bamFile) + "_PSfilter.bam");
-		//check output filename is valid
-		}else{
-			//check ext
-			try{
-				if(!"bam".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use BAM extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) +  ".bam\n";
+			// check output filename is valid
+		} else {
+			// check ext
+			try {
+				if (!"bam".equals(ExtensionFileFilter.getExtension(output))) {
+					r += "(!)Use BAM extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
+							+ ".bam\n";
 				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use BAM extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) +  ".bam\n"; }
-			//check directory
-				if(output.getParent()==null){
+			} catch (NullPointerException e) {
+				r += "(!)Output filename must have extension: use BAM extension for output filename. Try: "
+						+ ExtensionFileFilter.stripExtension(output) + ".bam\n";
+			}
+			// check directory
+			if (output.getParent() == null) {
 // 					System.err.println("default to current directory");
-				} else if(!new File(output.getParent()).exists()){
-					r += "(!)Check output directory exists: " + output.getParent() + "\n";
-				}
+			} else if (!new File(output.getParent()).exists()) {
+				r += "(!)Check output directory exists: " + output.getParent() + "\n";
+			}
 		}
-		
-		//check filter string is valid ATCG
+
+		// check filter string is valid ATCG
 		Pattern seqPat = Pattern.compile("[ATCG]+");
-		Matcher m = seqPat.matcher( filterString );
-		if( !m.matches() ){
-			r += "(!)Filter string must be formatted as a nucleotide sequence.\n" + filterString +
-				" is not a valid nucleotide sequence.\nExpected input string format: \"[ATCG]\"";
+		Matcher m = seqPat.matcher(filterString);
+		if (!m.matches()) {
+			r += "(!)Filter string must be formatted as a nucleotide sequence.\n" + filterString
+					+ " is not a valid nucleotide sequence.\nExpected input string format: \"[ATCG]\"";
 		}
-		
-		return(r);
+
+		return (r);
 	}
 }

src/cli/BAM_Manipulation/MergeBAMCLI.java

@@ -13,6 +13,7 @@
 	description = ToolDescriptions.merge_bam_description + "\n"+
 		"@|bold **Please run the picard tool directly:**|@ \n"+
 		"@|bold,yellow 'java -jar picard.jar MergeSamFiles'|@",
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)
 public class MergeBAMCLI implements Callable<Integer> {

src/cli/BAM_Manipulation/SortBAMCLI.java

@@ -13,6 +13,7 @@
 	description = ToolDescriptions.sort_bam_description + "\n"+
 		"@|bold **Please run the samtools tool directly:**|@ \n"+
 		"@|bold,yellow 'samtools sort -o <output.bam> <input.bam>'|@",
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)
 public class SortBAMCLI implements Callable<Integer> {