Example #1
0
function fasta($n)
{
    $iub = array(array('a', 0.27), array('c', 0.12), array('g', 0.12), array('t', 0.27), array('B', 0.02), array('D', 0.02), array('H', 0.02), array('K', 0.02), array('M', 0.02), array('N', 0.02), array('R', 0.02), array('S', 0.02), array('V', 0.02), array('W', 0.02), array('Y', 0.02));
    $homosapiens = array(array('a', 0.302954942668), array('c', 0.1979883004921), array('g', 0.1975473066391), array('t', 0.3015094502008));
    $alu = 'GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG' . 'GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA' . 'CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT' . 'ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA' . 'GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG' . 'AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC' . 'AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA';
    makeCumulative($iub);
    makeCumulative($homosapiens);
    makeRepeatFasta('ONE', 'H**o sapiens alu', $alu, $n * 2);
    makeRandomFasta('TWO', 'IUB ambiguity codes', $iub, $n * 3);
    makeRandomFasta('THREE', 'H**o sapiens frequency', $homosapiens, $n * 5);
}
Example #2
0
            $lineLength = $n;
        }
        if ($i + $lineLength < $sLength) {
            print substr($s, $i, $lineLength);
            print "\n";
            $i += $lineLength;
        } else {
            print substr($s, $i);
            $i = $lineLength - ($sLength - $i);
            print substr($s, 0, $i);
            print "\n";
        }
        $n -= $lineLength;
    }
}
/* Main -- define alphabets, make 3 fragments */
$iub = array('a' => 0.27, 'c' => 0.12, 'g' => 0.12, 't' => 0.27, 'B' => 0.02, 'D' => 0.02, 'H' => 0.02, 'K' => 0.02, 'M' => 0.02, 'N' => 0.02, 'R' => 0.02, 'S' => 0.02, 'V' => 0.02, 'W' => 0.02, 'Y' => 0.02);
$homosapiens = array('a' => 0.302954942668, 'c' => 0.1979883004921, 'g' => 0.1975473066391, 't' => 0.3015094502008);
$alu = 'GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG' . 'GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA' . 'CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT' . 'ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA' . 'GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG' . 'AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC' . 'AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA';
$n = 1000;
if ($_SERVER['argc'] > 1) {
    $n = $_SERVER['argv'][1];
}
makeCumulative($iub);
makeCumulative($homosapiens);
echo ">ONE H**o sapiens alu\n";
makeRepeatFasta($alu, $n * 2);
echo ">TWO IUB ambiguity codes\n";
makeRandomFasta($iub, $n * 3);
echo ">THREE H**o sapiens frequency\n";
makeRandomFasta($homosapiens, $n * 5);
Example #3
0
    $lineLength = LINE_LENGTH;
    while ($n > 0) {
        if ($n < $lineLength) {
            $lineLength = $n;
        }
        if ($i + $lineLength < $sLength) {
            print substr($s, $i, $lineLength);
            print "\n";
            $i += $lineLength;
        } else {
            print substr($s, $i);
            $i = $lineLength - ($sLength - $i);
            print substr($s, 0, $i);
            print "\n";
        }
        $n -= $lineLength;
    }
}
/* Main -- define alphabets, make 3 fragments */
$iub = array(array('a', 0.27), array('c', 0.12), array('g', 0.12), array('t', 0.27), array('B', 0.02), array('D', 0.02), array('H', 0.02), array('K', 0.02), array('M', 0.02), array('N', 0.02), array('R', 0.02), array('S', 0.02), array('V', 0.02), array('W', 0.02), array('Y', 0.02));
$homosapiens = array(array('a', 0.302954942668), array('c', 0.1979883004921), array('g', 0.1975473066391), array('t', 0.3015094502008));
$alu = 'GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG' . 'GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA' . 'CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT' . 'ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA' . 'GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG' . 'AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC' . 'AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA';
$n = 1000;
if ($_SERVER['argc'] > 1) {
    $n = $_SERVER['argv'][1];
}
makeCumulative(&$iub);
makeCumulative(&$homosapiens);
makeRepeatFasta('ONE', 'H**o sapiens alu', $alu, $n * 2);
makeRandomFasta('TWO', 'IUB ambiguity codes', $iub, $n * 3);
makeRandomFasta('THREE', 'H**o sapiens frequency', $homosapiens, $n * 5);