Initial commit

README.md

+# FASTA2AGP
+
+_FASTA2AGP_ is a command line program written in [Java](https://docs.oracle.com/javase/8/docs/technotes/guides/language/index.html) that allows creating [AGP](https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/) and contig sequence files from a FASTA-formatted scaffold sequence file.
+
+## Compilation and execution
+
+The source code of _FASTA2AGP_ is inside the _src_ directory and could be compiled and executed in two different ways. 
+
+#### Building an executable jar file
+
+On computers with [Oracle JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html) (6 or higher) installed, a Java executable jar file could be created. In a command-line window, go to the _src_ directory and type:
+```bash
+javac FASTA2AGP.java 
+echo Main-Class: FASTA2AGP > MANIFEST.MF 
+jar -cmvf MANIFEST.MF FASTA2AGP.jar FASTA2AGP.class 
+rm MANIFEST.MF FASTA2AGP.class 
+```
+This will create the executable jar file `FASTA2AGP.jar` that could be launched with the following command line model:
+```bash
+java -jar FASTA2AGP.jar [options]
+```
+
+#### Building a native code binary
+
+On computers with the [GNU compiler GCJ](https://gcc.gnu.org/onlinedocs/gcc-4.2.4/gcj/) installed, a binary could also be built. In a command-line window, go to the _src_ directory, and type:
+```bash
+make
+```
+This will create the executable binary file `FASTA2AGP` that could be launched with the following command line model:
+```bash
+./FASTA2AGP [options]
+```
+
+## Usage
+
+Launch _FASTA2AGP_ without option to read the following documentation:
+
+```
+ USAGE:  FASTA2AGP -i <scaffolds.fasta> [-o <contigs.fasta>] [-a <info.agp>] [-n <length>]
+
+  where options are:
+
+   -i <infile>   FASTA-formatted scaffold sequence file (mandatory)
+   -o <outfile>  FASTA-formatted contig sequence output file name (default: <infile>.fna)
+   -a <outfile>  AGP-formatted output file name (default: <infile>.agp)
+   -n <integer>  minimum length of scaffolding stretch of Ns (default: 10)
+```

src/FASTA2AGP.java

+/*
+  ####################################################################
+  FASTA2AGP: creating agp and contig sequence files from a FASTA-
+             formatted scaffold sequence file
+
+  [Version 1.2.180515ac]
+
+  Copyright (C) 2015,2016,2018  Alexis Criscuolo 
+
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation,  either version 3  of the License,  or
+  (at your option) any later version.
+  
+  This program is distributed in the hope that it will be useful,  but
+  WITHOUT  ANY  WARRANTY;   without  even  the   implied  warranty  of
+  MERCHANTABILITY or  FITNESS FOR  A PARTICULAR  PURPOSE.  See the GNU 
+  General Public License for more details.
+  
+  You should have  received a copy  of the GNU  General Public License
+  along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+  Contact: 
+  Institut Pasteur
+  Bioinformatics and Biostatistics Hub
+  C3BI, USR 3756 IP CNRS
+  Paris, FRANCE
+
+  alexis.criscuolo@pasteur.fr
+  ####################################################################
+*/
+import java.io.*;
+import java.util.*;
+public class FASTA2AGP {
+    // constants
+    static String NOFILE = "N.O.F.I.L.E";
+    // options
+    static File infile;  // -i
+    static File ctgFile; // -o
+    static File agpFile; // -a
+    static int polyNlgt; // -n
+    // io
+    static BufferedReader in;
+    static BufferedWriter outc, outa;
+    // data
+    static int size;
+    static ArrayList<String> fh, sq;
+    // stuffs
+    static int o, i, s, sN, eN, l, cptctg, part_number, base;
+    static String line, hdr, polyN;
+    static StringBuilder sb;
+    public static void main(String[] args) throws IOException {
+	// ############################
+	// ### man              #######
+	// ############################
+	if ( args.length < 2 ) {
+	    System.out.println(""); System.out.println(" USAGE:  FASTA2AGP -i <scaffolds.fasta> [-o <contigs.fasta>] [-a <info.agp>] [-n <length>]");
+	    System.out.println(""); System.out.println("  where options are:"); System.out.println(""); 
+	    System.out.println("   -i <infile>   FASTA-formatted scaffold sequence file (mandatory)");
+	    System.out.println("   -o <outfile>  FASTA-formatted contig sequence output file name (default: <infile>.fna)");
+	    System.out.println("   -a <outfile>  AGP-formatted output file name (default: <infile>.agp)");
+	    System.out.println("   -n <integer>  minimum length of scaffolding stretch of Ns (default: 10)");
+	    System.out.println(""); System.exit(0);
+	}
+	// ############################
+	// ### parsing options  #######
+	// ############################
+	infile = new File(NOFILE); 
+	ctgFile = new File(NOFILE);
+	agpFile = new File(NOFILE);
+	polyNlgt = 10;
+	o = -1;
+	while ( ++o < args.length ) {
+	    if ( args[o].equals("-i") ) { infile = new File(args[++o]); continue; }
+	    if ( args[o].equals("-o") ) { ctgFile = new File(args[++o]); continue; }
+	    if ( args[o].equals("-a") ) { agpFile = new File(args[++o]); continue; }
+	    if ( args[o].equals("-n") ) {
+		try { polyNlgt = Integer.parseInt(args[++o]); }
+		catch ( NumberFormatException e ) { System.out.println("incorrect integer value: " + args[o] + " (option -n)"); System.exit(1); }
+		if ( polyNlgt < 1 ) { System.out.println("incorrect integer value: " + polyNlgt + " (option -n)"); System.exit(1); }
+		continue;
+	    }
+	}
+	if ( ! infile.exists() ) { System.out.println(infile.toString() + " not found (options -i)"); System.exit(1); }
+	if ( ctgFile.toString().equals(NOFILE) ) ctgFile = new File(infile.toString() + ".fna");	
+	if ( agpFile.toString().equals(NOFILE) ) agpFile = new File(infile.toString() + ".agp");
+	sb = new StringBuilder(""); s = polyNlgt; while ( --s >= 0 ) sb = sb.append('N'); polyN = sb.toString();	
+	// ############################
+	// ### reading infile  ########
+	// ############################
+	fh = new ArrayList<String>(); sq = new ArrayList<String>(); sb = new StringBuilder(""); in = new BufferedReader(new FileReader(infile));
+	while ( true ) {
+	    try { line = in.readLine().trim(); } catch ( NullPointerException e ) { in.close(); break; }
+	    if ( line.startsWith(">") ) { if ( sb.length() != 0 ) { sq.add(sb.toString()); sb = new StringBuilder(""); } fh.add(line); continue; }
+	    sb = sb.append(line);
+	}
+	if ( sb.length() != 0 ) sq.add(sb.toString());
+	size = fh.size(); o = 10; while ( o < size ) o *= 10; base = ("" + (o *= 10)).length();
+	// ##############################
+	// ### writing outfiles  ########
+	// ##############################
+	outc = new BufferedWriter(new FileWriter(ctgFile)); outa = new BufferedWriter(new FileWriter(agpFile)); cptctg = 0; i = -1;
+	while ( ++i < size ) {
+	    line = sq.get(i).toUpperCase(); l = line.length(); s = 0; sN = line.indexOf(polyN);
+	    if ( s == -1 ) {
+		hdr = "contig_" + frmt(++cptctg,base); outc.write(">" + hdr); outc.newLine(); outc.write(line); outc.newLine();
+		// =======================================================================================================================================================
+		//          object                           object_beg  object_end  part_number  component_type  component_id   component_beg  component_end  orientation
+		//          |                                |           |           |            |               |              |              |              |
+		outa.write("scaffold_" + frmt(i+1,base) + "\t1\t" +      l +      "\t1\t" +      "W\t" +          hdr +       "\t1\t" +         l +         "\t+"); 
+		outa.newLine();
+		continue;
+	    }
+	    part_number = 0;
+	    while ( sN != -1 ) {
+		eN = sN; while ( (++eN < l) && (line.charAt(eN) == 'N') ) {}
+		// ========================================================
+		//        s                  sN               eN
+		//        |                  |                |
+		//  ...NNNAACTGTCACTACGAATGCTNNNNNNNNNNNNNNNNNACGTACGT
+		hdr = "contig_" + frmt(++cptctg,base); outc.write(">" + hdr); outc.newLine(); outc.write(line.substring(s, sN)); outc.newLine();
+		// =====================================================================================================================================================================
+		//          object                               object_beg     object_end  part_number          component_type  component_id  component_beg  component_end  orientation
+		//          |                                    |              |           |                    |               |             |              |              |
+		outa.write("scaffold_" + frmt(i+1,base) + "\t" + (s+1) + "\t" + sN + "\t" + (++part_number) + "\tW\t" +          hdr +      "\t1\t" +         (sN-s) +    "\t+"); outa.newLine();
+		// ============================================================================================================================================================
+		//          object                               object_beg      object_end  part_number          component_type gap_length   gap_type  linkage   link.evidence
+		//          |                                    |               |           |                    |              |            |         |         |
+		outa.write("scaffold_" + frmt(i+1,base) + "\t" + (sN+1) + "\t" + eN + "\t" + (++part_number) + "\tN\t" +         (eN-sN) + "\tscaffold\tyes\t" + "paired-ends"); outa.newLine();
+		s = eN; sN = line.indexOf(polyN, s);
+	    }
+	    // =====================================
+	    //        s                  
+	    //        |                  
+	    //  ...NNNAACTGTCACTACGAATGCTACGTACGT
+	    hdr = "contig_" + frmt(++cptctg,base); outc.write(">" + hdr); outc.newLine(); outc.write(line.substring(s)); outc.newLine();
+	    // ======================================================================================================================================================================
+	    //          object                               object_beg     object_end  part_number          component_type  component_id   component_beg  component_end  orientation
+	    //          |                                    |              |           |                    |               |              |              |              |
+	    outa.write("scaffold_" + frmt(i+1,base) + "\t" + (s+1) + "\t" + l + "\t" +  (++part_number) + "\tW\t" +          hdr +       "\t1\t" +         (l-s) +     "\t+"); outa.newLine();
+	}
+	outc.close(); outa.close();
+    }
+    static String frmt( int x, int base ) { return Integer.toString((int)(Math.pow(10, base) + x)).substring(1); }
+}

src/Makefile

+GCJ=gcj
+GCJFLAGS=-fsource=1.6 -march=native -msse2 -O3 -minline-all-stringops -fomit-frame-pointer -momit-leaf-frame-pointer -fstrict-aliasing -fno-store-check -fno-bounds-check -funroll-all-loops -Wall 
+OTHERFLAGS=-funsafe-math-optimizations -ffast-math
+MAIN=FASTA2AGP
+EXEC=FASTA2AGP
+
+FASTA2AGP: FASTA2AGP.java
+	$(GCJ) $(GCJFLAGS) --main=$(MAIN) $(MAIN).java -o $(EXEC)