create BEDUtilities for FASTAExtract

create a new class for shared methods to be used across script classes, starting with FASTAExtract's loadCoord method.

This static method loads a BED file into an ArrayList of BEDCoord objects.

Other minor changes:
- CLI PrintStream object set to STDERR

src/cli/Sequence_Analysis/FASTAExtractCLI.java

@@ -42,7 +42,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		FASTAExtract script_obj = new FASTAExtract(genomeFASTA, bedFile, output, forceStrand, bedHeader, null);
+		FASTAExtract script_obj = new FASTAExtract(genomeFASTA, bedFile, output, forceStrand, bedHeader, System.err);
 		script_obj.run();
 
 		System.err.println("Extraction Complete.");

src/scripts/Sequence_Analysis/FASTAExtract.java

@@ -10,10 +10,9 @@
 import java.io.IOException;
 import java.io.PrintStream;
 import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Scanner;
 
 import util.FASTAUtilities;
+import util.BEDUtilities;
 
 public class FASTAExtract {
 	private File GENOME = null;
@@ -41,19 +40,16 @@ public FASTAExtract(File gen, File b, File out, boolean str, boolean head, Print
 	}
 
 	public void run() throws IOException, InterruptedException {
-
-		if (PS == null)
-			PS = System.err;
-		System.out.println("STRAND:" + STRAND);
-		System.out.println("COORD:" + HEADER);
+		PS.println("STRAND:" + STRAND);
+		PS.println("COORD:" + HEADER);
 
 		try {
 			IndexedFastaSequenceFile QUERY = new IndexedFastaSequenceFile(GENOME);
 			PS.println("Proccessing File: " + BED.getName());
 			// Open Output File
 			OUT = new PrintStream(OUTFILE);
 
-			ArrayList<BEDCoord> BED_Coord = loadCoord(BED);
+			ArrayList<BEDCoord> BED_Coord = BEDUtilities.loadCoord(BED, HEADER);
 
 			for (int y = 0; y < BED_Coord.size(); y++) {
 				try {
@@ -76,47 +72,5 @@ public void run() throws IOException, InterruptedException {
 		} catch (SAMException e) {
 			PS.println(e.getMessage());
 		}
-
-	}
-
-	public ArrayList<BEDCoord> loadCoord(File INPUT) throws FileNotFoundException {
-		Scanner scan = new Scanner(INPUT);
-		ArrayList<BEDCoord> COORD = new ArrayList<BEDCoord>();
-		while (scan.hasNextLine()) {
-			String[] temp = scan.nextLine().split("\t");
-			if (temp.length > 2) {
-				if (!temp[0].contains("track") && !temp[0].contains("#")) {
-					String name = "";
-
-					if (!HEADER) { // create genomic coordinate name if requested
-						if (temp.length > 5) {
-							name = temp[0] + ":" + temp[1] + "-" + temp[2] + "(" + temp[5] + ")";
-						} else {
-							name = temp[0] + ":" + temp[1] + "-" + temp[2] + "(.)";
-						}
-					} else { // else create name based on BED file name or create one if non-existent
-						if (temp.length > 3) {
-							name = temp[3];
-						} else {
-							name = temp[0] + ":" + temp[1] + "-" + temp[2] + "(" + temp[5] + ")";
-						}
-					}
-
-					if (Integer.parseInt(temp[1]) >= 0) {
-						if (temp[5].equals("+")) {
-							COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "+",
-									name));
-						} else {
-							COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "-",
-									name));
-						}
-					} else {
-						System.out.println("Invalid Coordinate in File!!!\n" + Arrays.toString(temp));
-					}
-				}
-			}
-		}
-		scan.close();
-		return COORD;
 	}
 }

src/util/BEDUtilities.java

@@ -0,0 +1,82 @@
+package util;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.zip.GZIPInputStream;
+
+import objects.CoordinateObjects.BEDCoord;
+
+/**
+ * Class containing a set of shared methods to be used across script classes.
+ * 
+ * @author Olivia Lang
+ * @see scripts.Sequence_Analysis.FASTAExtract
+ */
+public class BEDUtilities {
+
+	/**
+	 * Load a list of BEDCoord objects from a file.
+	 * 
+	 * @param INPUT  the BED-formatted input file to load
+	 * @param HEADER the style of FASTA-header to use for the output (true = BED
+	 *               coord name, false = use Genomic Coordinate)
+	 * @return
+	 * @throws IOException 
+	 * @throws UnsupportedEncodingException 
+	 */
+	public static ArrayList<BEDCoord> loadCoord(File input, boolean HEADER) throws UnsupportedEncodingException, IOException {
+		ArrayList<BEDCoord> COORD = new ArrayList<BEDCoord>();
+		// Check if file is gzipped and instantiate appropriate BufferedReader
+		BufferedReader br;
+		if (GZipUtilities.isGZipped(input)) {
+			br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(input)), "UTF-8"));
+		} else {
+			br = new BufferedReader(new InputStreamReader(new FileInputStream(input), "UTF-8"));
+		}
+		// Initialize line variable to loop through
+		String line = br.readLine();
+		while (line != null) {
+			String[] temp = line.split("\t");
+			if (temp.length > 2) {
+				if (!temp[0].contains("track") && !temp[0].contains("#")) {
+					String name = "";
+
+					if (!HEADER) { // create genomic coordinate name if requested
+						if (temp.length > 5) {
+							name = temp[0] + ":" + temp[1] + "-" + temp[2] + "(" + temp[5] + ")";
+						} else {
+							name = temp[0] + ":" + temp[1] + "-" + temp[2] + "(.)";
+						}
+					} else { // else create name based on BED file name or create one if non-existent
+						if (temp.length > 3) {
+							name = temp[3];
+						} else {
+							name = temp[0] + ":" + temp[1] + "-" + temp[2] + "(" + temp[5] + ")";
+						}
+					}
+
+					if (Integer.parseInt(temp[1]) >= 0) {
+						if (temp[5].equals("+")) {
+							COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "+",
+									name));
+						} else {
+							COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "-",
+									name));
+						}
+					} else {
+						System.out.println("Invalid Coordinate in File!!!\n" + Arrays.toString(temp));
+					}
+				}
+			}
+			line = br.readLine();
+		}
+		br.close();
+		return COORD;
+	}
+}