Ed's Big Plans

Computing for Science and Awesome

C & Bioinformatics: ASCII Nucleotide Comparison Circuit

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Here’s a function I developed for Andre about a week ago. The C function takes two arguments. Both arguments are C characters. The first argument corresponds to a degenerate nucleotide as in the below table. The second argument corresponds to a non-degenerate nucleotide {‘A’, ‘C’, ‘G’, ‘T’} or any nucleotide ‘N’. The function returns zero if the logical intersection between the two arguments is zero. The function returns a one-hot binary encoding for the logical intersection if it exists so that {‘A’ = 1, ‘C’ = 2, ‘G’ = 4, ‘T’ = 8} and {‘N’ = 15}. All of this is done treating the lower 5-bits of the ASCII encoding for each character as wires of a circuit.

Character ASCII
(Low 5-Bits)
Represents One Hot Equals
A
00001
A 0001
1
B 00010 CGT 1110
14
C 00011 C 0010
2
D 00100 AGT 1101
13
G 00111 G 0100
4
H 01000 ACT 1011
11
K
01011 GT 1100
12
M 01101 AC 0011
3
N 01110 ACGT 1111
15
R 10010 AG 0101 5
S 10011 GC 0110
6
T 10100 T
1000
8
V 10110 ACG
0111
7
W 10111 AT
1001
9
Y 11001 CT
1010
10

The premise is that removing all of the logical branching and using only binary operators would make things a bit faster — I’m actually not sure if the following solution is faster because there are twelve variables local to the function scope — we can be assured that at least half of these variables will be stored outside of cache and will have to live in memory. We’d get a moderate speed boost if at all.

/*
    f():
        Bitwise comparison circuit that treats nucleotide and degenerate
        nucleotide ascii characters as mathematical sets.
        The operation performed is set i intersect j.
    arg char i:
        Primer -- accepts ascii |ABCDG HKMNR STVWY| = 15.
    arg char j:
        Sequence -- accepts ascii |ACGTN| = 5.
    return char (k = 0):
        false -- i intersect j is empty.
    return char (k > 0):
        1 -- the intersection is 'A'
        2 -- the intersection is 'C'
        4 -- the intersection is 'G'
        8 -- the intersection is 'T'
       15 -- the intersection is 'N'
    return char (undefined value):
        ? -- if any other characters are placed in i or j.
*/
char f(char i, char j) {

    // break apart Primer into bits ...
    char p = (i >> 4) &1;
    char q = (i >> 3) &1;
    char r = (i >> 2) &1;
    char s = (i >> 1) &1;
    char t =  i       &1;

    // break apart Sequence into bits ...
    char a = (j >> 4) &1;
    char b = (j >> 3) &1;
    char c = (j >> 2) &1;
    char d = (j >> 1) &1;
    char e =  j       &1;

    return

    ( // == PRIMER CIRCUIT ==
        ( // -- A --
            ((p|q|r|s  )^1) &         t |
            ((p|q|  s|t)^1) &     r     |
            ((p|  r|s|t)^1) &   q       |
            ((p|    s  )^1) &   q&r&  t |
            ((p|      t)^1) &   q&r&s   |
            ((  q|    t)^1) & p&s       |
            ((  q      )^1) & p&r&s
        )
        |
        ( // -- C --
            ((p|q|r    )^1) &       s   |
            ((p|  r|s|t)^1) &   q       |
            ((p|    s  )^1) &   q&r&  t |
            ((p|      t)^1) &   q&r&s   |
            ((  q|r    )^1) &       s&t |
            ((  q|    t)^1) & p  &r&s   |
            ((    r|s  )^1) & p&q&    t
        ) << 1
        |
        ( // -- G --
            ((  q|r|  t)^1) &       s   |
            ((p|q|  s|t)^1) &     r     |
            ((p|q      )^1) &     r&s&t |
            ((p|  r    )^1) &   q&  s&t |
            ((p|      t)^1) &   q&r&s   |
            ((  q|r    )^1) & p&    s   |
            ((  q|    t)^1) & p&    s
        ) << 2
        |
        ( // -- T --
            ((p|q|r|  t)^1) &       s   |
            ((  q|  s|t)^1) &     r     |
            ((p|  r|s|t)^1) &   q       |
            ((p|  r    )^1) &   q&  s&t |
            ((p|      t)^1) &   q&r&s   |
            ((  q      )^1) & p&  r&s&t |
            ((    r|s  )^1) & p&q&    t
        ) << 3
    )
    &
    ( // == SEQUENCE CIRCUIT ==
        ( // -- A --
            ((a|b|c|d  )^1) &         e |
            ((a|      e)^1) &   b&c&d
        )
        |
        ( // -- C --
            ((a|b|c    )^1) &       d&e |
            ((a|      e)^1) &   b&c&d
        ) << 1
        |
        ( // -- G --
            ((a|b      )^1) &     c&d&e |
            ((a|      e)^1) &   b&c&d
        ) << 2
        |
        ( // -- T --
            ((a|      e)^1) &   b&c&d   |
            ((  b|  d|e)^1) & a&  c
        ) << 3
    );
}

Andre’s eventual solution was to use a look-up table which very likely proves faster in practice. At the very least, this was a nice refresher and practical example for circuit logic using four sets of minterms (one for each one-hot output wire).

Should you need this logic to build a fast physical circuit or have some magical architecture with a dozen registers (accessible to the compiler), be my guest 😀

Eddie Ma

February 27th, 2011 at 11:49 pm

The Right Tool (Why I chose Java to do RSA)

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Brief: I learned something valuable last week when working on this RSA encryption/decryption assignment for my Computer Security class. It’s important to be versatile when doing computer science — we must ensure we always use the most efficient tool. If we aren’t versatile, we risk taking tremendous amounts of time trying to reimplement something that already exists elsewhere.

So, what tool is the right tool to quickly throw together RSA encryption?

It turns out that Java does an excellent job. Its BigInteger class has all the ingredients you’ll ever need.

// This function generates a new probable prime ...
BigInteger p = BigInteger.probablePrime(bits, random);

// This function performs modulus inverse ...
BigInteger d = e.modInverse(phi_n);

// These functions can be used to check your work ...
BigInteger one = d.multiply(e).mod(phi_n);
BigInteger one = p.gcd(q);

// This function is at the heart of RSA ...
BigInteger C = M.modPow(d, n);

Before I looked at the Java documentation, I had plans to do this with Python and some of my classmates had plans with MATLAB. It’s not that these are inherently bad technologies — they’re just not the right tool.

As much as I have gripes with Java, I’ve got to say that this made me and a lot of my class very happy 😀

Eddie Ma

February 24th, 2011 at 6:26 pm

Posted in Pure Programming

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C & Math: Sieve of Eratosthenes with Wheel Factorization

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In the first assignment of Computer Security, we were to implement The Sieve of Eratosthenes. The instructor gives a student the failing grade of 6/13 for a naive implementation, and as we increase the efficiency of the sieve, we get more marks. There are the three standard optimizations: (1) for the current prime being considered, start the indexer at the square of the current prime; (2) consider only even numbers; (3) end crossing out numbers at the square root of the last value of the sieve.

Since the assignment has been handed in, I’ve decided to post my solution here as I haven’t seen C code on the web which implements wheel factorization.

We can think of wheel factorization as an extension to skipping all even numbers. Since we know that all even numbers are multiples of two, we can just skip them all and save half the work. By the same token, if we know a pattern of repeating multiples corresponding to the first few primes, then we can skip all of those guaranteed multiples and save some work.

The wheel I implement skips all multiples of 2, 3 and 5. In Melissa O’Neill’s The Genuine Sieve of Erastothenes, an implementation of the sieve with a priority queue optimization is shown in Haskell while wheel factorization with the primes 2, 3, 5 and 7 is discussed. The implementation of that wheel (and other wheels) is left as an exercise for her readers 😛

But first, let’s take a look at the savings of implementing this wheel. Consider the block of numbers in modulo thirty below corresponding to the wheel for primes 2, 3 and 5 …

0 1 2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25 26 27 28 29

Only the highlighted numbers need to be checked to be crossed out during sieving since the remaining values are guaranteed to be multiples of 2, 3 or 5. This pattern repeats every thirty numbers which is why I say that it is in modulo thirty. We hence skip 22/30 of all cells by using the wheel of thirty — a savings of 73%. If we implemented the wheel O’Neill mentioned, we would skip 77% of cells using a wheel of 210 (for primes 2, 3, 5 and 7).

(Note that the highlighted numbers in the above block also correspond to the multiplicative identity one and numbers which are coprime to 30.)

Below is the final code that I used.

#include <stdlib.h>
#include <stdio.h>
#include <math.h>

const unsigned int SIEVE = 15319000;
const unsigned int PRIME = 990000;

int main(void) {
    unsigned char* sieve = calloc(SIEVE + 30, 1); // +30 gives us incr padding
    unsigned int thisprime = 7;
    unsigned int iprime = 4;

    unsigned int sieveroot = (int)sqrt(SIEVE) +1;

    // Update: don't need to zero the sieve - using calloc() not malloc()

    sieve[7] = 1;

    for(; iprime < PRIME; iprime ++) {
        // ENHANCEMENT 3: only cross off until square root of |seive|.
        if(thisprime < sieveroot) {
            // ENHANCEMENT 1: Increment by 30 -- 4/15 the work.
            // ENHANCEMENT 2: start crossing off at prime * prime.
            int i = (thisprime * thisprime);
            switch (i % 30) { // new squared prime -- get equivalence class.
                case 1:
                    if(!sieve[i] && !(i % thisprime)) {sieve[i] = 1;}
                    i += 6;
                case 7:
                    if(!sieve[i] && !(i % thisprime)) {sieve[i] = 1;}
                    i += 4;
                case 11:
                    if(!sieve[i] && !(i % thisprime)) {sieve[i] = 1;}
                    i += 2;
                case 13:
                    if(!sieve[i] && !(i % thisprime)) {sieve[i] = 1;}
                    i += 4;
                case 17:
                    if(!sieve[i] && !(i % thisprime)) {sieve[i] = 1;}
                    i += 2;
                case 19:
                    if(!sieve[i] && !(i % thisprime)) {sieve[i] = 1;}
                    i += 4;
                case 23:
                    if(!sieve[i] && !(i % thisprime)) {sieve[i] = 1;}
                    i += 6;
                case 29:
                    if(!sieve[i] && !(i % thisprime)) {sieve[i] = 1;}
                    i += 1; // 29 + 1 (mod 30) = 0 -- just in step
            }
            for(; i < SIEVE; i += 30) {
                if(!sieve[i+1] && !((i+1) % thisprime)) sieve[i+1] = 1;
                if(!sieve[i+7] && !((i+7) % thisprime)) sieve[i+7] = 1;
                if(!sieve[i+11] && !((i+11) % thisprime)) sieve[i+11] = 1;
                if(!sieve[i+13] && !((i+13) % thisprime)) sieve[i+13] = 1;
                if(!sieve[i+17] && !((i+17) % thisprime)) sieve[i+17] = 1;
                if(!sieve[i+19] && !((i+19) % thisprime)) sieve[i+19] = 1;
                if(!sieve[i+23] && !((i+23) % thisprime)) sieve[i+23] = 1;
                if(!sieve[i+29] && !((i+29) % thisprime)) sieve[i+29] = 1;
            }
        }

        {
            int i = thisprime;
            switch (i % 30) { // write down the next prime in 'thisprime'.
                case 1:
                    if(!sieve[i]) {thisprime = i; sieve[i] = 1; goto done;}
                    i += 6;
                case 7:
                    if(!sieve[i]) {thisprime = i; sieve[i] = 1; goto done;}
                    i += 4;
                case 11:
                    if(!sieve[i]) {thisprime = i; sieve[i] = 1; goto done;}
                    i += 2;
                case 13:
                    if(!sieve[i]) {thisprime = i; sieve[i] = 1; goto done;}
                    i += 4;
                case 17:
                    if(!sieve[i]) {thisprime = i; sieve[i] = 1; goto done;}
                    i += 2;
                case 19:
                    if(!sieve[i]) {thisprime = i; sieve[i] = 1; goto done;}
                    i += 4;
                case 23:
                    if(!sieve[i]) {thisprime = i; sieve[i] = 1; goto done;}
                    i += 6;
                case 29:
                    if(!sieve[i]) {thisprime = i; sieve[i] = 1; goto done;}
                    i += 1;
            }
            for(; i < SIEVE; i += 30) {
                if(!sieve[i+1]) {thisprime = i+1; sieve[i+1] = 1; goto done;}
                if(!sieve[i+7]) {thisprime = i+7; sieve[i+7] = 1; goto done;}
                if(!sieve[i+11]) {thisprime = i+11; sieve[i+11] = 1; goto done;}
                if(!sieve[i+13]) {thisprime = i+13; sieve[i+13] = 1; goto done;}
                if(!sieve[i+17]) {thisprime = i+17; sieve[i+17] = 1; goto done;}
                if(!sieve[i+19]) {thisprime = i+19; sieve[i+19] = 1; goto done;}
                if(!sieve[i+23]) {thisprime = i+23; sieve[i+23] = 1; goto done;}
                if(!sieve[i+29]) {thisprime = i+29; sieve[i+29] = 1; goto done;}
            }
            done:;
        }
    }
    printf("%d\n", thisprime);
    free(sieve);
    return 0;
}

Notice that there is a switch construct — this is necessary because we aren’t guaranteed that the first value to sieve for a new prime (or squared prime) is going to be an even multiple of thirty. Consider sieving seven — the very first prime to consider. We start by considering 72 = 49. Notice 49 (mod 30) is congruent to 19. The switch statement incrementally moves the cursor from the 19th equivalence class to the 23rd, to the 29th before pushing it one integer more to 30 — 30 (mod 30) is zero — and so we are able to continue incrementing by thirty from then on in the loop.

The code listed is rigged to find the 990 000th prime as per the assignment and uses a sieve of predetermined size. Note that if you want to use my sieve code above to find whichever prime you like, you must also change the size of the sieve. If you take a look at How many primes are there? written by Chris K. Caldwell, you’ll notice a few equations that allow you to highball the nth prime of your choosing, thereby letting you calculate that prime with the overshot sieve size.

Note also that this sieve is not the most efficient. A classmate of mine implemented The Sieve of Atkin which is magnitudes faster than this implementation.

Eddie Ma

February 3rd, 2011 at 11:08 pm

C# & Science: A 2D Heatmap Visualization Function (PNG)

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Today, let’s take advantage of the bitmap writing ability of C# and output some heatmaps. Heatmaps are a nice visualization tool as they allow you to summarize numeric continuous values as colour intensities or hue spectra. It’s far easier for the human to grasp a general trend in data via a 2D image than it is to interpret a giant rectangular matrix of numbers. I’ll use two examples to demonstrate my heatmap code. The function provided is generalizable to all 2D arrays of doubles so I welcome you to download it and try it yourself.

>>> Attached: ( tgz | zip — C# source: demo main, example data used below, makefile ) <<<

Let’s start by specifying the two target colour schemes.

  • RGB-faux-colour {blue = cold, green = medium, red = hot} for web display
  • greyscale {white = cold, black = hot} suitable for print

Next, let’s take a look at the two examples.

Example Heat Maps 1: Bioinformatics Sequence Alignments — Backtrace Matrix

Here’s an application of heat maps to sequence alignments. We’ve visualized the alignment traces in the dynamic programming score matrices of local alignments. Here, a pair of tryptophan-aspartate-40 protein sequences are aligned so that you can quickly pick out two prominent traces with your eyes. The highest scoring spot is in red — the highest scoring trace carries backward and upward on a diagonal from that spot.

The left heatmap is shown in RGB-faux-colour decorated with a white diagonal. The center heatmap is shown in greyscale with no decorations. The right heatmap is decorated with a major diagonal, borders, lines every 100 values and ticks every ten values. Values correspond to amino acid positions where the top left is (0, 0) of the alignment.

Example Heat Maps 2: Feed Forward Back Propagation Network — Weight Training

Here’s another application of heat maps. This time we’ve visualized the training of neural network weight values. The weights are trained over 200 epochs to their final values. This visualization allows us to see the movement of weights from pseudorandom noise (top) to their final values (bottom).

Shown above are the weight and bias values for a 2-input, 4-hidden-node, 4-hidden-node, 2-output back-propagation feed-forward ANN trained on the toy XOR-EQ problem. The maps are rendered as RGB-faux-colour (left); greyscale (center); and RGB-faux-colour decorated with horizontal lines every 25 values (=50px) (right). Without going into detail, the leftmost 12 columns bridge inputs to the first hidden layer, the next 20 columns belong to the next weight layer, and the last 10 columns bridge to the output layer.

Update: I changed the height of the images of this example to half their original height — the horizontal lines now occur every 25 values (=25px).

C# Functions

This code makes use of two C# features — (1) function delegates and (2) optional arguments. If you also crack open the main file attached, you’ll notice I also make use of a third feature — (3) named arguments. A function delegate is used so that we can define and select which heat function to use to transform a three-tuple of double values (real, min, max) into a three-tuple of byte values (R, G, B). Optional arguments are used because the function signature has a total of twelve arguments. Leaving some out with sensible default values makes a lot of sense. Finally, I use named arguments in the main function because they allow me to (1) specify my optional arguments in a logical order and (2) read which arguments have been assigned without looking at the function signature.

Heat Functions

For this code to work, heat functions must match this delegate signature. Arguments: val is the current value, min is the lowest value in the matrix and max is the highest value in the matrix; we use min and max for normalization of val.

public delegate byte[] ValueToPixel(double val, double min, double max);

This is the RGB-faux-colour function that breaks apart the domain of heats and assigns it some amount of blue, green and red.

public static byte[] FauxColourRGB(double val, double min, double max) {
    byte r = 0;
    byte g = 0;
    byte b = 0;
    val = (val - min) / (max - min);
           if(               val <= 0.2) {
        b = (byte)((val / 0.2) * 255);
    } else if(val >  0.2 &&  val <= 0.7) {
        b = (byte)((1.0 - ((val - 0.2) / 0.5)) * 255);
    }
           if(val >= 0.2 &&  val <= 0.6) {
        g = (byte)(((val - 0.2) / 0.4) * 255);
    } else if(val >  0.6 &&  val <= 0.9) {
        g = (byte)((1.0 - ((val - 0.6) / 0.3)) * 255);
    }
           if(val >= 0.5               ) {
        r = (byte)(((val - 0.5) / 0.5) * 255);
    }
    return new byte[]{r, g, b};
}

This is a far simpler greyscale function.

public static byte[] Greyscale(double val, double min, double max) {
    byte y = 0;
    val = (val - min) / (max - min);
    y = (byte)((1.0 - val) * 255);
    return new byte[]{y, y, y};
}

Heatmap Writer

The function below is split into a few logical parts: (1) we get the minimum and maximum heat values to normalize intensities against; (2) we set the pixels to the colours we want; (3) we add the decorations (borders, ticks etc.); (4) we save the file.

public static void SaveHeatmap(
    string fileName, double[,] matrix, ValueToPixel vtp,
    int pixw = 1, int pixh = 1,
    Color? decorationColour = null,
    bool drawBorder = false, bool drawDiag = false,
    int hLines = 0, int vLines = 0, int hTicks = 0, int vTicks = 0)
{
    var rows = matrix.GetLength(0);
    var cols = matrix.GetLength(1);
    var bitmap = new Bitmap(rows * pixw, cols * pixh);

    //Get min and max values ...
    var min = Double.PositiveInfinity;
    var max = Double.NegativeInfinity;
    for(int i = 0; i < matrix.GetLength(0); i ++) {
        for(int j = 0; j < matrix.GetLength(1); j ++) {
            max = matrix[i,j] > max? matrix[i,j]: max;
            min = matrix[i,j] < min? matrix[i,j]: min;
        }
    }
    //Set pixels ...
    for(int j = 0; j < bitmap.Height; j ++) {
        for(int i = 0; i < bitmap.Width; i ++) {
            var triplet = vtp(matrix[i / pixw, j / pixh], min, max);
            var color = Color.FromArgb(triplet[0], triplet[1], triplet[2]);
            bitmap.SetPixel(i, j, color);
        }
    }
    //Decorations ...
    var dc = decorationColour ?? Color.Black;
    for(int i = 0; i < bitmap.Height; i ++) {
        for(int j = 0; j < bitmap.Width; j ++) {
            if(drawBorder) {
                if(i == 0 || i == bitmap.Height -1) {
                    // Top and Bottom Borders ...
                    bitmap.SetPixel(j, i, dc);
                } else if(j == 0 || j == bitmap.Width -1) {
                    // Left and Right Borders ...
                    bitmap.SetPixel(j, i, dc);
                }
            }
            if(bitmap.Width == bitmap.Height && drawDiag && (i % 2 == 0)) {
                // Major Diagonal ... (only draw if square image +explicit)
                bitmap.SetPixel(i, i, dc);
            }
            //Zeroed lines and zeroed ticks are turned off.
            if(hLines != 0 && i % (hLines*pixh) == 0) {
                if(j % (2*pixw) == 0) {
                    //Horizontal Bars ...
                    bitmap.SetPixel(j, i, dc);
                }
            } else if(hTicks != 0 && i % (hTicks*pixh) == 0) {
                // Dots: H-Spacing
                if(vTicks != 0 && j % (vTicks*pixw) == 0) {
                    // Dots: V-Spacing
                    bitmap.SetPixel(j, i, dc);
                }
            } else if(i % (2*pixh) == 0) {
                if(vLines != 0 && j % (vLines*pixw) == 0) {
                    //Vertical Bars
                    bitmap.SetPixel(j, i, dc);
                }
            }
        }
    }

    //Save file...
    bitmap.Save(fileName, ImageFormat.Png);
    bitmap.Dispose();
}

Happy mapping 😀

Compatibility Notes: The C# code discussed was developed with Mono using Monodevelop. All code is compatible with the C#.NET 4.0 specification and is forward compatible. I’ve linked in two assemblies — (1) -r:System.Core for general C#.Net 3.5~4.0 features, and (2) r:System.Drawing to write out PNG files. If you need an overview of how to set up Monodevelop to use the System.Drawing assembly, see C Sharp PNG Bitmap Writing with System.Drawing in my notebook.

Eddie Ma

January 21st, 2011 at 1:20 pm

Simple Interactive Phylogenetic Tree Sketches JS+SVG+XHTML

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>>> Attached: ( parse_newick_xhtml.js | draw_phylogeny.js — implementation in JS | index.html — demo with IL-1 ) <<<
>>> Attached: ( auto_phylo_diagram.tgz — includes all above, a python script, a demo makefile and IL-1 data ) <<<

In this post, I discuss a Python script I wrote that will convert a Newick Traversal and a FASTA file into a browser-viewable interactive diagram using SVG+JS+XHTML. This method is compatible with WebKit (Safari, Chrome) and Mozilla (Firefox) renderers but not Opera. XHTML doesn’t work with IE, so we’ll have to wait for massive adoption of HTML5 before I can make this work for everyone — don’t worry, it’s coming.

To the left is what the rendered tree looks like (shown as a screen captured PNG).

I recommend looking at the demo index.xhtml above if your browser supports it now. The demo will do a far better job than text in explaining exactly what features are possible using this method.

Try clicking on the different nodes and hyperlinks in the demo — notice that the displayed alignment strips away sites (columns) that are 100% gaps so that each node displays only a profile relevant for itself.

I originally intended to explain all the details of the JavaScripts that render and drive the diagram, but I think it’d be more useful to first focus on the Python script and the data input and output from the script.

The Attached Python Script to_xhtml.py found in auto_phylo_diagram.tgz

I’ll explain how to invoke to_xhtml.py with an example below.

python to_xhtml.py IL1fasta.txt IL1tree2.txt "IL-1 group from NCBI CDD (15)" > index.xhtml

Arguments …

  1. Plain Text FASTA file — IL1fasta.txt
  2. Plain Text Newick Traversal file — IL1tree2.txt
  3. Title of the generated XHTML — “IL-1 group from NCBI CDD (15)”

The data I used was generated with MUSCLE with default parameters. I specified the output FASTA with -out and the output second iteration tree with -tree2.

The Attached makefile found in auto_phylo_diagram.tgz

The makefile has two actual rules. If index.html does not exist, it will be regenerated with the above Python script and IL1fasta.txt and IL1tree2.txt. If either IL1fasta.txt or IL1tree2.txt or both do not exist, these files are regenerated using MUSCLE with default parameters on the included example data file ncbi.IL1.cl00094.15.fasta.txt. Running make on the included package shouldn’t do anything since all of the files are included.

The Example Data

The example data comes from the Interleukin-1 group (cd00100) from the NCBI Conserved Domains Database (CDD).

Finally, I’ll discuss briefly the nitty gritty of the JavaScripts found as stand-alones above that are also included in the package.

Part Two of Two

As is the nature of programatically drawing things, this particular task comes with its share of prerequisites.

In a previous — Part 1, I covered Interactive Diagrams Using Inline JS+SVG+XHTML — see that post for compatibility notes and the general method (remember, this technique is a holdover that will eventually be replaced with HTML5 and that the scripts in this post are not compatible with Opera anymore).

In this current post — Part 2, I’ll also assume you’ve seen Parsing a Newick Tree with recursive descent (you don’t need to know it inside and out, since we’ll only use these functions) — if you look at the example index.html attached, you’ll see that we actually parse the Newick Traversal using two functions in parse_newick_xhtml.jstree_builder() then traverse_tree(). The former converts the traversal to an in-memory binary tree while the latter accepts the root node of said tree and produces an array. This array is read in draw_phylogeny.js by fdraw_tree_svg() which does the actual rendering along with attaching all of the dynamic behaviour.

Parameters ( What are we drawing? )

To keep things simple, let’s focus on three requirements: (1) the tree will me sketched top-down with the root on top and its leaves below; (2) the diagram must make good use of the window width and avoid making horizontal scroll bars (unless it’s absolutely necessary); (3) the drawing function must make the diagram compatible with the overall document object model (DOM) so that we can highlight nodes and know what nodes were clicked to show the appropriate data.

Because of the second condition, all nodes in a given depth of the tree will be drawn at the same time. A horizontal repulsion will be applied so that each level will appear to be centre-justified.

General Strategy

Because we are centre-justifying the tree, we will be drawing each level of the tree simultaneously to calculate the offsets we want for each node. We perform this iteratively for each level of depth of the tree in the function fdraw_tree_svg(). Everything that is written dynamically by JavaScript goes to a div with a unique id. All of the SVG goes to id=”tree_display” and all of the textual output including raster images, text and alignments goes to id=”thoughts”. To attach behaviour to hyperlinks, whether it’s within the SVG or using standard anchor tags, the “onclick” property is defined. In this case, we always call the same function “onclick=javascript:select_node()“. This function accepts a single parameter: the integer serial number that has been clicked.

Additional Behaviour — Images and Links to Databases

After I wrote the first drafts of the JavaScripts, I decided to add two more behaviours in the current version. First, if a particular node name has the letters “GI” in it, the script will attempt to hyperlink it with the proceeding serial number against NCBI. Second, if a particular node name has the letters “PDB” in it, the script will attempt to hyperlink the following identifier against RSCB Protein Database and also pull the first thumbnail with an img tag for the 3D protein structure.

Enjoy!

This was done because I wanted to show a custom alignment algorithm to my advisors. In this demo, I’ve stripped away the custom alignment leaving behind a more general yet pleasing visualizer. I hope that the Python script and JavaScripts are useful to you. Enjoy!

Eddie Ma

January 1st, 2011 at 11:55 pm

C# & Bioinformatics: Edit Strings and Local Alignment Subprofiles

with 2 comments

Alternatively: The awful finite string manipulation bug that took me forever to fix.

Update: Code last update 2010 Dec. 12 (branch logic fixed: gave default “else” case highest priority instead).

Every so often, a bug creeps in during the implementation of a utility function that halts an entire project until it can be fixed. I bumped into one that was so insidious — so retrospectively obvious — that I must share it with you. This particular bug has to do with the way Edit Strings behave when you use them to represent changes done during a Local Alignment rather than a Global Alignment.

Those of you who have looked into MUSCLE may have seen the 2004 BMC paper that goes into great detail about its implementation. In it, Dr. Edgar describes Edit Strings (e-strings) — these are integer strings which keep track of the edits performed on a sequence in order to insert gaps in the correct locations corresponding to an alignment.

I’ve previously discussed and explained e-strings and their use in sequence alignment here and also how to convert alignment strings (a recording of site-to-site insertions/deletions/substitutions) to edit strings here.

E-Strings in Local Alignments

E-strings weren’t originally designed with local alignments in mind — but that’s OK. We can make a few adjustments that will let us keep track of gaps the way we intend them. In a global alignment, all tokens (characters) in each of the aligned sequences are considered. In a local alignment, we need to be able to specify two aligned subsequences rather than the alignment of two full sequences. We can add a simple integer offset to indicate the number of positions since the beginning of aligned sequences to specify the start position of each subsequence.

These are two sequences s and t — (to keep things easy to visualize, I’ve just used characters from the English alphabet).

s = DEIJKLMNOPQRSTUVWXYZ
t = ABCDEFGHIJKLMNOUVWXY

Assume that the following is the optimal global alignment of s and t.

s(global) = ---DE---IJKLMNOPQRSTUVWXYZ
t(global) = ABCDEFGHIJKLMNO-----UVWXY-

The corresponding edit strings for s and t are es and et respectively.

e(s, global) = < -3, 2, -3, 18 >
e(t, global) = < 15, -5, 5, -1 >

Remember, we can take the sum of the absolute values in two edit strings corresponding to the same alignment to be sure that they contain the number of sites. This is true because a site in a given sequence or profile must be either an amino acid (in a sequence) or a distribution of amino acids (in a profile) or a gap (in either). In this case, the absolute values of both es and et correctly add up to 26.

Now let’s adapt the above to local alignments.

The corresponding optimal local alignment for s and t is as follows.

s(local) = DE---IJKLMNOPQRSTUVWXY
t(local) = DEFGHIJKLMNO-----UVWXY

The edit strings only need an offset to specify the correct start position in each sequence. Remember that our indexing is zero based, so the position for the character “A” was at position zero.

e(s, local) = 3 + < 2, -3, 17 >
e(t, local) = 3 + < 12, -5, 5 >

It’s a pretty straight forward fix. Notice that the absolute values of the integers inside the vectors now only sum up to 22 (corresponding to the sites stretching from “D” to “Y”).

Local Alignment E-String Subprofiles

The bug I faced wasn’t in the above however. It only occurred when I needed to specify subprofiles of local alignments. Imagine having a local alignment of two sequences in memory. Imagine now that there is a specific run of aligned sites therein that you are interested in and want to extract. That specific run should be specifiable by using the original sequences and a corresponding pair of e-strings and pair of offsets. Ideally, the new e-strings and offsets should be derived from the e-strings and offsets we had gathered from performing the original local alignment. We call this specific run of aligned sites a subprofile.

As you will see, this bug is actually a result of forgetting to count the number of gaps needed that occur after the original local alignment offset and before where the new subprofile should start. Don’t worry, this will become clearer with an example.

For the local alignment of s and t, I want to specify a subprofile stretching from the site at letter “I” to the site at letter “V”.

s(local) = DE---IJKLMNOPQRSTUVWXY → s(subprofile) = IJKLMNOPQRSTUV
t(local) = DEFGHIJKLMNO-----UVWXY → t(subprofile) = IJKLMNO-----UV

What do you suppose the edit string to derive would be?

Let’s puzzle this out — we want to take a substring from each s and t from position 5 to position 18 of the local alignment as shown below …

Position:       0    0            1  2
                0    5            8  1
     s(local) = DE---IJKLMNOPQRSTUVWXY →
s(subprofile) =      IJKLMNOPQRSTUV
                |    |            |  |
     t(local) = DEFGHIJKLMNO-----UVWXY →
t(subprofile) =      IJKLMNO-----UV
                     |            |
                     |<-  Want  ->|

Let’s break this down further and get first the vector part of the e-string and then the offset part of the e-string.

Getting the Vector part of the Edit String

Remember, we’re trying to get an edit string that will operate on the original sequences s, t and return ssubprofile, tsubprofile. Getting the vector part of the estring is straight forward, you literally find all of the sites specified in the subsequence and save them. Since we want positions [5, 18] in the local edit strings, we retrieve the parts of the edit strings which correspond to those sites (we’ll ignore offsets for now). To visualize this site-to-site mapping, let’s decompose our local estrings into something I call unit-estrings — an equivalent estring which only uses positive and negative ones (given as “+” and “-” below in the unit vectors us, ut for s, t respectively).

Position:                                0         0                         1     2
                                         0         5                         8     1
    s(local) =                           D E - - - I J K L M N O P Q R S T U V W X Y
e(s, vector) = < 2, -3, 17 > -> u(s) = < + + - - - + + + + + + + + + + + + + + + + + >
e(s, newvec) = < 14 >        <-        <           + + + + + + + + + + + + + +       >
                                                   |<-        want!        ->|
e(t, newvec) = < 7, -5, 2 >  <-        <           + + + + + + + - - - - - + +       >
e(t, vector) = < 12, -5, 5 > -> u(t) = < + + + + + + + + + + + + - - - - - + + + + + >
    t(local) =                           D E F G H I J K L M N O - - - - - U V W X Y

We retrieve as our new vectors es, newvec = < 14 > and et, newvec = < 7, -5, 2 >. Notice that the integer vector elements are just a count of the runs of positive and negative ones in the subprofile region that we want.

Getting the Offset part of the Edit String (the Right way)

This part gets a bit tricky. The offset is a sum of three items.

  1. The offset from the original sequence to the local alignment.
  2. The offset from the local alignment to the subprofile.
  3. The negative of all of the gap characters that are inserted in the local alignment until the start of the subprofile.

The below diagram shows where each of these values come from.

            s =    DEIJKLMNOPQRSTUVWXYZ
     s(local) =    DE---IJKLMNOPQRSTUVWXY -> +0 -- offset from original to local
s(subprofile) =    .....IJKLMNOPQRSTUV    -> +5 -- offset from local to subprofile
                     ---                  -> -3 -- gaps: local start to subprofile start
                                          => +2 == TOTAL
                        |            |
            t = ABCDEFGHIJKLMNOUVWXY
     t(local) = ...DEFGHIJKLMNO-----UVWXY -> +3 -- offset from original to local
t(subprofile) =    .....IJKLMNO-----UV    -> +5 -- offset from local to subprofile
                                          -> -0 -- gaps: local start to subprofile start
                                          => +8 == TOTAL

You might be wondering about the weird gap subtraction for sequence s. This is the solution to my bug! We need this gap subtraction! When you forget to subtract these gaps, you end up with an alignment that is incorrect where the subprofile of s starts too late. But why is this so? When we transform a sequence from the original to the subprofile, the gaps that we’ve taken for granted in the local alignment don’t exist yet. This way, we would be mistakenly pushing our subprofile into a position where non-existent gapped sites are virtually aligned to existing amino acid sites in the alignment partner t. This was a very odd concept for me to grasp, so let yourself think on this for a bit if it still doesn’t make sense. … You could always take it for granted too once I show you below that this is indeed the correct solution 😛

The completed edit strings to specify the subprofile from “I” to “V” for the local alignment of s and t are thus:

e(s, subprofile) = 2 + < 14 >
e(t, subprofile) = 8 + < 7, -5, 2 >

So let’s make sure these work — let’s apply es, subprofile and et, subprofile onto s and t to see if we get back the correct subprofiles.

>>> apply offsets ...

s = DEIJKLMNOPQRSTUVWXYZ : +2 remaining ...
s = IJKLMNOPQRSTUVWXYZ

t = ABCDEFGHIJKLMNOUVWXY : +8 remaining ...
t = IJKLMNOUVWXY

>>> apply e-strings ...

s = IJKLMNOPQRSTUVWXYZ : < 14 > remaining ...
s = IJKLMNOPQRSTUV

t = IJKLMNOUVWXY : < 7, -5, 2 > remaining ...
t = IJKLMNO : UVWXY : < -5, 2 > remaining ...
t = IJKLMNO----- : UVWXY : < 2 > remaining ...
t = IJKLMNO-----UV

s = IJKLMNOPQRSTUV -- selected subprofile ok.
t = IJKLMNO-----UV -- selected subprofile ok.

The above application results in the desired subprofile.

The SubEString Function in C#

The below source code gives the correct implementation in order to find the e-string corresponding to a subprofile with the following arguments. It is an extension function for List<int> — a natural choice since I am treating lists of integer type as edit strings in my project.

  1. this List<int> u — the local alignment e-string from which to create the subprofile e-string.
  2. int start — the offset from the left specifying the location of the subprofile with respect to the local alignment.
  3. int end_before — the indexed site before which we stop; this is different from length since start and end_before are zero-based and are specified from the very start of the local alignment.
  4. out int lostGaps — returns a negative value to add to the offset — this is the number of gaps that occur between the start of the local alignment and the start of the subprofile.

This function returns a new List<int> e-string as you would expect.

public static List<int> SubEString(
     this List<int> u, int start, int end_before, out int lostGaps) {

    if(end_before < start) {
        Console.Error.WriteLine("Error: end_before < start?! WHY?");
        throw new ValueOutOfRange();
    }

    var retObj = new List<int>();
    var consumed = 0; // the amount "consumed" so far.
    var remaining_start = start; // subtract "remaining_start" to zero.
    var ui = 0; // the current index in the e-string
    var uu = 0; // the current element of the e-string
    var uu_abs = 0; // the absolute value of the current element
    lostGaps = 0; // the number of gaps that is subtracted from the offset.

    //START -- dealing with the "start" argument ...
    for(; ui < u.Count; ui ++) {
        uu = u[ui];
        uu_abs = Math.Abs(uu);
        if(uu_abs < remaining_start) {
            if(uu < 0) lostGaps += uu; //LOSTGAPS
            // add uu this time
            // it's the fraction of remaining_start we care about.
            consumed += uu_abs; // uu smaller than start amount, eat uu.
            remaining_start -= uu_abs; // start shrinks by uu.
            uu_abs = 0; // no uu left.
            uu = 0; // no uu left.
            // not done -- go back and get more uu for me to eat.
        }
        else if(consumed + uu_abs == remaining_start) {
            if(uu < 0) lostGaps += -remaining_start; //LOSTGAPS
            // -- if thus uu is equal to the start amount,
            // count them into LOSTGAPS
            // we want to get everything occurring before the subestring start
            consumed += remaining_start; // same size -- consume start amount.
            uu_abs = 0; // MAD (mutually assured destruction 0 -> 0)
            remaining_start = 0; // MAD
            uu = 0; // MAD
            ui ++; break; // done.
        }
        else if(consumed + uu_abs > remaining_start) {
            if(consumed + uu_abs > end_before && consumed < remaining_start) {
                // easier to say ui == u.Count-1?
                if(uu < 0) lostGaps += -remaining_start; //LOSTGAPS
                uu_abs = (end_before - (consumed + remaining_start));
                uu = uu > 0 ? uu_abs : -uu_abs;
                retObj.Add(uu);
                return retObj;
            } else if(consumed + uu_abs < end_before) {
                consumed += uu_abs;
                // Seemingly wrong -- however:
                // push all the way to the end; subtract the beginning of uu_abs
                // ensures correct calculation of remaining string
                uu_abs -= remaining_start; // remove only start amount.
                // we're getting the end half of uu_abs!
                if(uu < 0) lostGaps += -remaining_start; //LOSTGAPS
                remaining_start = 0; // no start left.
                uu = uu > 0 ? uu_abs : -uu_abs; // remaining uu at this ui.
                if(uu != 0) retObj.Add(uu); // fixes a zero-entry bug
                ui ++; break; // done.
            } else {
                if(uu < 0) lostGaps += -remaining_start; //LOSTGAPS
                uu_abs = (end_before - remaining_start);
                uu = uu > 0 ? uu_abs : -uu_abs;
                retObj.Add(uu);
                return retObj;
            }
        }
    }

    //END_BEFORE -- dealing with the "end_before" argument ...
    for(; ui < u.Count; ui ++) {
        uu = u[ui];
        uu_abs = Math.Abs(uu);
        if((consumed + uu_abs) == end_before) {
            retObj.Add(uu);
            break;
        } else if((consumed + uu_abs) < end_before) {
            retObj.Add(uu);
            consumed += uu_abs;
        } else /*if((consumed + uu_abs) > end_before)*/ {
            uu_abs = end_before - consumed;
            uu = uu > 0 ? uu_abs : -uu_abs;
            retObj.Add(uu);
            break;
        }
    }
    return retObj;
}

I’ve really sent the above code through unit tests and also in practical deployment so it should be relatively bug free. I hope that by posting this here, you can tease out the logic from both the code and the comments and port it to your preferred language. In retrospect, maybe this bug wasn’t so obvious after all. When you think about it, each of the pieces of code and logic are doing exactly what we asked them to. It was only in chaining together an e-string subprofile function along with a local alignment that this thing ever even popped out. Either way, the fix is here. Hopefully it’ll be helpful.

Two Important Notes

  • Since global alignments represent the aligned sites of all sequences involved, no offset is used and hence this bug would never occur when specifying a subprofile of a global alignment.
  • Gaps that occur in the original sequence don’t affect retrieving the subprofile e-string calculation at all because those gaps DO exist and can be authentically counted into an offset.

Next

I haven’t had a need yet for porting the multiply function (earlier post) from global alignment logic to local alignment logic. If there are any insidious logical flaws like the ones I encountered this time, I’ll be sure to make a post.