ABI Chromatograms

[Bailey Kessing]

We are trying to generate the chromatogram for an ABI DNA sequencing file. Biojava (http://biojava.org) has a jar that will do this and many other things for DNA sequence files. Not sure how technical I need to be but a chromatogram is basically an image of the DNA detecting on the sequencing machine. I need to generate that image. I have attached the Jar and a sequencing file ("t1.ab1" as an example) and the Java code we are trying to get to work (with not a lot of success). We think we are close, but have a couple of errors. Anyone care to take a look and see if a fresh set of eyes will help? THANKS!!!

 

 

####Code below#####

 

import java.awt.image.BufferedImage;

import java.awt.Color;

import java.awt.Graphics2D;

import java.awt.Rectangle;

import java.awt.RenderingHints;

import java.io.IOException;

import java.io.File;

import java.io.FileNotFoundException;

import java.util.Iterator;

import javax.imageio.ImageIO;

import javax.imageio.ImageWriter;

import javax.imageio.stream.FileImageOutputStream;

import org.biojava.bio.chromatogram.Chromatogram;

import org.biojava.bio.chromatogram.ChromatogramFactory;

import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;

import org.biojava.bio.chromatogram.graphic.ChromatogramGraphic;

import org.biojava.bio.program.abi.ABIFChromatogram

import org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

import org.biojava.bio.chromatogram.*

import org.biojava.bio.chromatogram.graphic.*

import org.biojava.bio.program.abi.*;

import org.biojava.bio.*;

import org.biojava.bio.program.abi.*;

import org.biojava.bio.seq.*;

import org.biojava.bio.seq.impl.*;

import org.biojava.bio.seq.io.*;

import org.biojava.bio.symbol.*;

 

int OUT_HEIGHT = 240;

float OUT_HORIZ_SCALE = 2.0f;

 

File infile = new File('/Users/kessingb/Desktop/Chromatogram/t1.ab1');

//return infile

 

String name = infile.getName()

 

ABITrace trace = new ABITrace(infile)

//return trace.getSequenceLength()

return trace.getTraceLength()

 

Chromatogram c = ABIFChromatogram.create(infile)

//Chromatogram c = ChromatogramFactory.create(infile)

 

String outExt = "png";

Iterator writers = ImageIO.getImageWritersBySuffix(outExt);

ImageWriter iw = (ImageWriter) writers.next();

 

        /* build output stream */

        

File outfile = new File('/Users/kessingb/Desktop/Chromatogram/t1.jpg');

//FileImageOutputStream out = new FileImageOutputStream(outfile);

 

        

ChromatogramGraphic gfx = new ChromatogramGraphic(trace);

gfx.setHeight(OUT_HEIGHT);

gfx.setHorizontalScale(OUT_HORIZ_SCALE);

//set some options that affect the output

// turn off filled-in "callboxes"

gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE);

gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE);

gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE);

gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE);

gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER, Boolean.FALSE);

//this option controls whether each trace/callbox/etc is scaled/positioned

        // individually, or whether the scaling is done on all shapes at the level

        // of the graphics context

        // enabling this option is recommended for higher-quality output

gfx.setOption(ChromatogramGraphic.Option.USE_PER_SHAPE_TRANSFORM, Boolean.TRUE);

        

        /* create output image */

 

        BufferedImage bi = new BufferedImage(

                                   gfx.getWidth(), 

                                   gfx.getHeight(), 

                                   BufferedImage.TYPE_INT_RGB);

        Graphics2D g2 = bi.createGraphics();

        g2.setBackground(Color.white);

        g2.clearRect(0, 0, bi.getWidth(), bi.getHeight());

 

        /* draw chromatogram into image */

 

        // turn on AA for nicer output

        //g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);

        // the main event

        gfx.drawTo(g2);

        // work-around an OS X bug where sometimes the last Shape drawn

        // doesn't show up in the output

        g2.draw(new java.awt.Rectangle(-10, -10, 5, 5));

 

        /* write image out */

 

        iw.setOutput(outfile);

biojava-1.7.1.jar

t1.ab1

[john renfrew]

Bailey

heres some code which works...
simplified where appropriate

<code>

import java.awt.image.BufferedImage
import java.awt.Color
import java.awt.Graphics2D
import java.awt.Rectangle
import java.awt.RenderingHints
import javax.imageio.ImageIO
import org.biojava.bio.chromatogram.Chromatogram
import org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
import org.biojava.bio.program.abi.ABIFChromatogram
import org.biojava.bio.program.abi.ABITrace

OUT_HEIGHT = 240
OUT_HORIZ_SCALE = 2.0f

infile = new File('path/to/file')
//return infile

name = infile.getName()

trace = new ABITrace(infile)

c = ABIFChromatogram.create(infile)

    /* build output stream */
   
outfile = new File('/Users/whoever/documents/t1.jpg')
   
//ERROR in this line
gfx = new ChromatogramGraphic(c)
gfx.setHeight(OUT_HEIGHT)
gfx.setHorizontalScale(OUT_HORIZ_SCALE)
//set some options that affect the output
// turn off filled-in "callboxes"
gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE)
gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE)
gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE)
gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE)
gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER, Boolean.FALSE)
//this option controls whether each trace/callbox/etc is scaled/positioned
    // individually, or whether the scaling is done on all shapes at the level
    // of the graphics context
    // enabling this option is recommended for higher-quality output
gfx.setOption(ChromatogramGraphic.Option.USE_PER_SHAPE_TRANSFORM, Boolean.TRUE)
   
//return 888
    /* create output image */

bi = new BufferedImage( gfx.getWidth(), gfx.getHeight(), BufferedImage.TYPE_INT_RGB)
g2 = bi.createGraphics()
g2.setBackground(Color.white)
g2.clearRect(0, 0, bi.getWidth(), bi.getHeight())

    /* draw chromatogram into image */

    // turn on AA for nicer output
    //g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON)
    // the main event
gfx.drawTo(g2)
    // work-around an OS X bug where sometimes the last Shape drawn
    // doesn't show up in the output
g2.draw(new java.awt.Rectangle(-10, -10, 5, 5))

    /* write image out */

try{
    ImageIO.write(bi, 'jpg', outfile)
} catch (e) {
    return e.getMessage()
}
return true
//OR return the image to a container
return bi

</code>

 

Edited September 2, 2015 by john renfrew

[Bailey Kessing]

Thanks so much!!! I will give it a try right away!!!

[Bailey Kessing]

OK John, I am still getting an error…let me see what I can ferret out…

Oh, here is the error I am getting: 

org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:

Script1.groovy: 18: unexpected char: 0xA0 @ line 18, column 1.

      /* build output stream */

   ^

 

1 error

 

 

Parameters:

{}

[David Wikström]

0xA0 is an invalid character you sometimes get when posting code from online resources etc. Try using e.g. a text editor to do a search/replace on all occurrences, and then paste the code back into FileMaker.

[Bailey Kessing]

Ah, thanks. I should have thought of that!!! Will give it a try!!

[john renfrew]

the new forum does not have  proper code black like the older version which used to allow for copy without the extra characters...

It is the Unicode Character 'NO-BREAK SPACE' (U+00A0)

 

john

[Bailey Kessing]

Hey gang, thanks a lot for your hep!!! That was it. When I put in my text viewer it was giving the same looking code that a regular space was so I didn't notice it at first…should have, but hell, I am a scientist !!  Anyways, it is perfect now, thanks so much for all the help!!!

[Bailey Kessing]

If I wanted to read from a file that was stored in a container...

I am trying to use nfile = fmpro.getContainerStream("Demo::read container") but don't seem to have the syntax correct...

[john renfrew]

syntax is right

comment out the trace = new ABI trace line

I then get an EOF problem with the ab1 file though. This is >>Signals that an end of file or end of stream has been reached unexpectedly during input.

but from the Api >>Due to the non-single-pass design of the ABI format, this method will wrap the InputStream in an CachingInputStream. For this reason, create(File) should be preferred

[Bailey Kessing]

Yeah, that is what I am getting also.