[Biophp-dev] sample
Can Tran
biophp-dev@bioinformatics.org
Mon, 29 Mar 2004 22:12:43 -0800
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Hi,
Sorry about my late start in biophp development.
I've been pretty busy with work.
Just wanted to run a sample function by you guys to see
if it meets coding standard. I wasn't sure if you had any
coding conventions.
Best wishes,
can
<?php
function hydropathy($sequence, $window, &$x, &$y)
{
$aminoacids = array(
"G"=>-0.400, "A"=>1.800, "V"=>4.200, "L"=>3.800,
"I"=>4.500, "M"=>1.900, "F"=>2.800, "P"=>-1.600,
"S"=>-0.800, "T"=>-0.700, "C"=>2.500, "N"=>-3.500,
"Q"=>-3.500, "Y"=>-1.300, "W"=>-0.900, "D"=>-3.500,
"E"=>-3.500, "H"=>-3.200, "K"=>-3.900, "R"=>-4.500
);
$midpt = ($window + 1) / 2;
$length = strlen($sequence);
for($i = 0; $i < $length - $window; $i++)
{
$total = 0;
for($j = 0; $j < $window; $j++)
{
$total = $total + $aminoacids[$sequence[$i + $j]];
}
$total = $total / $window;
$x[$i] = $i + $midpt;
$y[$i] = $total;
if($total > $max)
{
$max = $total;
}
if($total < $min)
{
$min = $total;
}
}
}
$sequence =
"MPPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGREQERRGHFVRHSEKAAEEAYTRTTRALHERFDRLERMLDDNRR";
hydropathy($sequence, 19, $array1, $array2);
echo "<PRE>";
for($i = 0; $i < count($array1); $i++)
{
echo "$array1[$i] \t $array2[$i] \n";
}
echo "</PRE>";
?>
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<!doctype html public "-//W3C//DTD W3 HTML//EN">
<html><head><style type="text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
--></style><title>sample</title></head><body>
<div>Hi,</div>
<div>Sorry about my late start in biophp development.</div>
<div>I've been pretty busy with work.</div>
<div>Just wanted to run a sample function by you guys to see</div>
<div>if it meets coding standard. I wasn't sure if you had any</div>
<div>coding conventions.</div>
<div>Best wishes,</div>
<div>can</div>
<div><br></div>
<div><tt><font size="-2" color="#000000"><?php<br>
<br>
</font><font size="-2" color="#760F50">function</font><font size="-2"
color="#000000"> hydropathy($sequence, $window, &$x, &$y)<br>
{<br>
<br>
<x-tab> </x-tab>$aminoacids =</font><font size="-2" color="#760F50">
array</font><font size="-2" color="#000000">(<br>
</font><font size="-2" color="#891315">
"G"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-0.400</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"A"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">1.800</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"V"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">4.200</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"L"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">3.800</font><font size="-2"
color="#000000">,<br>
</font><font size="-2" color="#891315">
"I"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">4.500</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"M"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">1.900</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"F"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">2.800</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"P"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-1.600</font><font size="-2"
color="#000000">,<br>
</font><font size="-2" color="#891315">
"S"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-0.800</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"T"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-0.700</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"C"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">2.500</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"N"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-3.500</font><font size="-2"
color="#000000">,<br>
</font><font size="-2" color="#891315">
"Q"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-3.500</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"Y"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-1.300</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"W"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-0.900</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"D"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-3.500</font><font size="-2"
color="#000000">,<br>
</font><font size="-2" color="#891315">
"E"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-3.500</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"H"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-3.200</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"K"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-3.900</font><font size="-2"
color="#000000">,</font><font size="-2" color="#891315">
"R"</font><font size="-2" color="#000000">=></font><font
size="-2" color="#0000FF">-4.500</font><font size="-2"
color="#000000"><br>
);<br>
<x-tab> </x-tab><br>
<x-tab> </x-tab>$midpt =
($window +</font><font size="-2" color="#0000FF"> 1</font><font
size="-2" color="#000000">) /</font><font size="-2" color="#0000FF">
2</font><font size="-2" color="#000000">;<br>
<x-tab> </x-tab>$length =
strlen($sequence);<br>
<x-tab> </x-tab></font><font size="-2"
color="#760F50">for</font><font size="-2" color="#000000">($i
=</font><font size="-2" color="#0000FF"> 0</font><font size="-2"
color="#000000">; $i < $length - $window; $i++)<br>
<x-tab> </x-tab>{<br>
<x-tab>
</x-tab><x-tab>
</x-tab>$total =</font><font size="-2" color="#0000FF"> 0</font><font
size="-2" color="#000000">;<br>
<x-tab>
</x-tab><x-tab>
</x-tab></font><font size="-2" color="#760F50">for</font><font
size="-2" color="#000000">($j =</font><font size="-2" color="#0000FF">
0</font><font size="-2" color="#000000">; $j < $window; $j++)<br>
<x-tab> </x-tab><x-tab>
</x-tab>{<br>
<x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>$total = $total + $aminoacids[$sequence[$i + $j]];<br>
<x-tab>
</x-tab><x-tab>
</x-tab>}<br>
<x-tab>
</x-tab><x-tab>
</x-tab>$total = $total / $window;<br>
<x-tab>
</x-tab><x-tab> </x-tab><br>
<x-tab>
</x-tab><x-tab>
</x-tab>$x[$i] = $i + $midpt;<br>
<x-tab>
</x-tab><x-tab>
</x-tab>$y[$i] = $total;<br>
<x-tab>
</x-tab><x-tab> </x-tab><br>
<x-tab>
</x-tab><x-tab>
</x-tab></font><font size="-2" color="#760F50">if</font><font
size="-2" color="#000000">($total > $max)<br>
<x-tab>
</x-tab><x-tab>
</x-tab>{<br>
<x-tab>
</x-tab><x-tab>
</x-tab><x-tab> </x-tab>$max
= $total;<br>
<x-tab> </x-tab><x-tab>
</x-tab>}<br>
<x-tab>
</x-tab><x-tab> </x-tab><br>
<x-tab>
</x-tab><x-tab>
</x-tab></font><font size="-2" color="#760F50">if</font><font
size="-2" color="#000000">($total < $min)<br>
<x-tab>
</x-tab><x-tab>
</x-tab>{ <br>
<x-tab>
</x-tab><x-tab>
</x-tab><x-tab> </x-tab>$min
= $total;<br>
<x-tab> </x-tab><x-tab>
</x-tab>}<br>
<x-tab> </x-tab>}<br>
}<br>
<br>
<br>
<br>
$sequence =</font><font size="-2" color="#891315">
"MPPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYP<span
></span
>RALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGREQERRGHFVRHSEK<span
></span>AAEEAYTRTTRALHERFDRLERMLDDNRR"</font><font size="-2"
color="#000000">;<br>
<br>
hydropathy($sequence,</font><font size="-2" color="#0000FF">
19</font><font size="-2" color="#000000">, $array1, $array2);<br>
</font><font size="-2" color="#760F50">echo</font><font size="-2"
color="#891315"> "<PRE>"</font><font size="-2"
color="#000000">;<br>
</font><font size="-2" color="#760F50">for</font><font size="-2"
color="#000000">($i =</font><font size="-2" color="#0000FF">
0</font><font size="-2" color="#000000">; $i < count($array1);
$i++)<br>
{<br>
<x-tab> </x-tab></font><font
size="-2" color="#760F50">echo</font><font size="-2" color="#891315">
"$array1[$i] \t $array2[$i] \n"</font><font size="-2"
color="#000000">;<br>
}<br>
</font><font size="-2" color="#760F50">echo</font><font size="-2"
color="#891315"> "</PRE>"</font><font size="-2"
color="#000000">;<br>
?></font></tt></div>
</body>
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