Tryag File Manager

/home/cluster1/data/bu01/1121861/jlex/alignment/align.php

<?
set_time_limit(1000);
error_reporting(0);

function reverse_complement($s) {
    $complements = array("A"=>"T","T"=>"A","C"=>"G","G"=>"C"," "=>" ");
    $s = strtoupper($s);
    $s = strrev($s);
    $length = strlen($s);
    $rc = "";
    for($i=0;$i<$length;$i++) {
	$rc .= $complements[$s[$i]];
    }
    return $rc;
}

function translate($s, $frame) {
    $aas = array("TTT"=>"F","TTC"=>"F","TTA"=>"L","TTG"=>"L","TCT"=>"S","TCC"=>"S",
		 "TCA"=>"S","TCG"=>"S","TAT"=>"Y","TAC"=>"Y","TAA"=>"*","TAG"=>"*",
		 "TGT"=>"C","TGC"=>"C","TGA"=>"*","TGG"=>"W","CTT"=>"L","CTC"=>"L",
		 "CTA"=>"L","CTG"=>"L","CCT"=>"P","CCC"=>"P","CCA"=>"P","CCG"=>"P",
		 "CAT"=>"H","CAC"=>"H","CAA"=>"Q","CAG"=>"Q","CGT"=>"R","CGC"=>"R",
		 "CGA"=>"R","CGG"=>"R","ATT"=>"I","ATC"=>"I","ATA"=>"I","ATG"=>"M",
		 "ACT"=>"T","ACC"=>"T","ACA"=>"T","ACG"=>"T","AAT"=>"N","AAC"=>"N",
		 "AAA"=>"K","AAG"=>"K","AGT"=>"S","AGC"=>"S","AGA"=>"R","AGG"=>"R",
		 "GTT"=>"V","GTC"=>"V","GTA"=>"V","GTG"=>"V","GCT"=>"A","GCC"=>"A",
		 "GCA"=>"A","GCG"=>"A","GAT"=>"D","GAC"=>"D","GAA"=>"E","GAG"=>"E",
		 "GGT"=>"G","GGC"=>"G","GGA"=>"G","GGG"=>"G");

$length = strlen($s);
    $aa_sequence = "";
    for($i=$frame-1;$i<$length;$i+=3) {
	$codon = substr($s,$i,3);
	if(array_key_exists($codon,$aas)) {
	    $aa_sequence .= $aas[$codon];
	}
	else {
	    $aa_sequence .= "?";
	}
    }
    return $aa_sequence;
}

function aligned_to_unaligned($aligned_seqs) {
    $seqs = array();
    foreach($aligned_seqs as $name=>$seq) {
	$seq = ereg_replace("-","",$seq);
	$seqs[$name] = $seq;
    }
    return $seqs;
}

function load_clustal_file($file_name) {
    $in = fopen($file_name,"r");
    fgets($in);
    fgets($in);

$seqs = array();
    while($line = fgets($in)) {
	if((ereg("[*]",$line)) || ((strlen($line) > 2) && (trim($line) == ""))) {
	    $line = substr($line,0,-2);
	    $length = strlen($line);
	    $start = $length - $num_cols;
	    $s = substr($line,($num_cols*-1));
	    $seqs["identity"] .= $s;
	}
	else if(trim($line) != "") {
	    $line = trim($line);
	    $index = strrpos($line," ");
	    $name = trim(substr($line,0,$index));	    
	    $seq = trim(substr($line,$index));
	    $length = strlen($seq);
	    $num_cols = $length;
	    $seqs[$name] .= $seq;
	}
	$prev_line = trim($line);
    }
    fclose($in);
    return $seqs;    
}

function align_sequences($sequences, $file_name) {
    $out = fopen("alignments/".$file_name.".txt","w");
    foreach($sequences as $name=>$sequence) {
	fwrite($out,">".$name."\n".$sequence."\n");
    }
    fclose($out);
    exec("clustalw.exe alignments/".$file_name.".txt");
    $seqs = load_clustal_file("alignments/".$file_name.".aln");
    return $seqs;
}

$stats[$name][$cur_name]["length"] = $length;
			$stats[$name][$cur_name]["num_same"] = $num_same;
			$stats[$name][$cur_name]["num_bps"] = $seq_num_bps;
			$stats[$name][$cur_name]["num_identities"] = $num_identities;
		    }
		    else {
			$stats[$cur_name][$name]["length"] = "-";
			$stats[$cur_name][$name]["num_same"] = "-";
			$stats[$cur_name][$name]["num_bps"] = "-";
			$stats[$cur_name][$name]["num_identities"] = "-";
		    }
		}
	    }
	}
    }
    return $stats;
}

function display_stats($stats) {
    $fields = "";
    $cols = "<tr><th></th>";
    foreach($stats as $name=>$stat_set) {	
	$cols .= "<th>$name</th>";
	$fields .= "<tr><th>$name</th>";
	foreach($stat_set as $nums) {
	    $length = $nums["length"];
	    $num_same = $nums["num_same"];
	    $num_bps = $nums["num_bps"];
	    $num_identities = $nums["num_identities"];
	    $percent = round((($num_same/$length)*100),1);
	    $identity = round((($num_identities/$num_bps)*100),1);

$fields .= "<td align='center'>$percent% : $num_same / $length<BR> $identity% : $num_identities / $num_bps</td>";
	}
	$fields .= "</tr>";
    }
    $cols .= "</tr>";
    $table = "<html><table border='1'>$cols $fields </table>";
    echo $table;
}
    
    
function make_blast_link($seq) {
    $seq = ereg_replace("-","",$seq);
    $length = strlen($seq);
    $temp = ereg_replace("[DEFHIKLMNPQRS]","",$seq);
    $temp_length = strlen($temp);	
    if((.75*$length) > $temp_length) {
	$program = "blastp";
	$page = "Proteins";
    }
    else {
	$program = "blastn";
	$page = "Nucleotides";
    }
    $blast_link = "<a href='http://www.ncbi.nih.gov/BLAST/Blast.cgi?CMD=Web&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&QUERY=".$seq."&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&NCBI_GI=on&PAGE=".$page."&PROGRAM=".$program."&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS.y=8&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes' target='_blast'>Blast!</a>";
    return $blast_link;
}

function display_report_form($file_name) {
    echo "<a href='align.php4?function=stats' target='_stats'>Display Statistics Report</a><BR>";
    echo "<br><br>";
    echo "<H2>Record Alignment Result</H2>";
    echo "<form action='align.php4' method='post'>";
    echo "<input type='hidden' name='function' value='record'/>";
    echo "<input type='hidden' name='file_name' value='$file_name'/>";
    echo "<table width='800'>";
    echo "<tr><th align='left' width='50'>Date:</th><td><input type='text' name='date' value='".date("Y-m-d")."'/>(YYYY-MM-DD)</td></tr>";
    echo "<tr><th colspan='2' align='left'>Purpose:</th></tr>";
    echo "<tr><td colspan='2'><textarea name='purpose' rows='2' cols='60'></textarea></td></tr>";
    echo "<tr><th colspan='2' align='left'>Conclusions:</th></tr>";
    echo "<tr><td colspan='2'><textarea name='conclusions' cols='80' rows='6'></textarea></td></tr>";
    echo "<tr><th colspan='2' align='left'>Plans:</th></tr>";
    echo "<tr><td colspan='2'><textarea name='plans' cols='80' rows='6'></textarea></td></tr>";
    echo "<tr><td colspan='2' align='center'><input type='submit' value='Record'></td></tr>";
    echo "</table></form>";
}

echo "<form action='align.php4' method='post'>";
    echo "<input type='hidden' name='function' value='realign'/>";
    echo "<input type='hidden' name='num_results' value='".count($seqs)."'/>";
    echo "Output Filename: <input type='text' size='30' name='file_name'/><br/>";
    echo "Font Size: <input type='text' size='10' name='font_size' value='8px'/>";
    
    echo "<table>";
    echo "<tr><th>Blast</th><th>Realign</th><th>RC</th><th>Name</th></tr>";
    echo $offsets;
    $row_num = 1;
    foreach($seqs as $name=>$seq) {
	$length = strlen($seq);
	$temp = ereg_replace("[DEFHIKLMNPQRS]","",$seq);
	$temp_length = strlen($temp);	
	if((.75*$length) > $temp_length) {
	    $colors = $aa_colors;
	}
	else {
	    $colors = $dna_colors;
	}
	$blast_link = make_blast_link($seq);
	echo "<tr><td>$blast_link</td>";
	echo "<td><input type='checkbox' name='realign_".$row_num."' value='on'/>";
	echo "<td><input type='checkbox' name='rc_".$row_num."' value='on'/></td>";
	echo "<td nowrap>$name<input type='hidden' name='name_".$row_num."' value='$name'/></td>";
	for($i=0;$i<$length;$i++) {
	    if(array_key_exists($seq[$i],$colors)) {
		$color = $colors[$seq[$i]];
	    }
	    echo "<td bgcolor='$color'><font style=\"font-size: $font_size\">".$seq[$i]."</font></td>";
	}
	echo "</tr>";
	$row_num++;
    }
    echo $offsets;
    echo "</table>";
    echo "Translate Sequences: <input type='checkbox' name='translate' value='on'/>";
    echo "Frame: <select name='frame'><option>1</option><option>2</option><option>3</option></select><BR/>";
    echo "<input type='submit'/>";
    echo "</form>";
}

echo "<form action='align.php4' method='post'>";
    echo "<input type='hidden' name='function' value='realign'/>";
    echo "<table>";
    
    $count = 0;
    $offset = 0;
    $num_rows = count($rows);
    for($j=0;$j<$num_rows;$j++) {
	$row = $rows[$j];
	if(($count % $num_seqs) == 0) {
	    $offsets = "";
	    for($i=0;$i<$cols;$i++) {
		if((($i+1)%21) == 0) {
		    $offset += 20;
		    $offsets .= "<td>$offset</td>";
		}
		else {
		    $offsets .= "<td>&nbsp;</td>";
		}
	    }
	    echo $offsets;
	}
	$count++;
	echo $row;
    }
    echo "</table>";
}

/* NOTE: This writes to an unclosed xml file. It must be closed upon adding it to MySQL */
function record_experiment($aligned_seqs) {    
    $date = $_POST["date"];	
    $purpose = $_POST["purpose"];
    $conclusions = $_POST["conclusions"];
    $plans = $_POST["plans"];
    $file_name = strtolower($_POST["file_name"]);

$out = fopen("../alignments.xml","a+");
    $close_tag = "</alignments>";
    $index = strlen($close_tag)*(-1);

fwrite($out,"\n");
    fwrite($out,"<alignment>\n");
    fwrite($out,"<date>$date</date>\n");
    fwrite($out,"<purpose>$purpose</purpose>\n");
    fwrite($out,"<file>$file_name</file>\n");    
    
    foreach($aligned_seqs as $name=>$seq) {
	if($name != "identity") {
	    $index = strpos($name,"-");
	    $strain = substr($name,0,$index);
	    $description = substr($name,$index+1);
	    fwrite($out,"<sequence>\n");
	    fwrite($out,"<strain>$strain</strain>\n");
	    fwrite($out,"<description>$description</description>\n");
	    fwrite($out,"</sequence>\n");
	}
    }
    fwrite($out,"<conclusions>$conclusions</conclusions>\n");
    fwrite($out,"<plans>$plans</plans>\n");
    fwrite($out,"</alignment>\n");
    fclose($out);
}

session_start();

$font_size = $_POST["font_size"];
$file_name = $_POST["file_name"];
$function = $_POST["function"];
if($function == "") {
    $function = $_GET["function"];
}

if($function == "realign") {    
    if(!array_key_exists("seqs",$_SESSION)) {
	die("No sequences to realign.<BR>");
    }
    $translate = trim($_POST["translate"]);
    
    $frame = $_POST["frame"];
    $old_seqs = $_SESSION["seqs"];
    $seqs = array();
    $num_sequences = $_POST["num_results"];
    for($i=1;$i<=$num_sequences;$i++) {	
	if($_POST["realign_".$i] == "on") {
	    $name = $_POST["name_".$i];
	    $seq = $old_seqs[$name];
	    if($_POST["rc_".$i] == "on") {
		$seq = reverse_complement($seq);
	    }
	    if($translate == "on") {
		$seq = translate($seq,$frame);
	    }
	    $seqs[$name] = $seq;
	}
    }
    $aligned_seqs = align_sequences($seqs,$file_name);
    $_SESSION["aligned_seqs"] = $aligned_seqs;
    display_alignment_horizontal($aligned_seqs,$font_size);
    display_report_form($file_name);
}
else if ($function == "record") {
    record_experiment($_SESSION["aligned_seqs"]);
    echo "Thank you for recording your data.<BR/>";
    echo "<a href='../add_database.php4?file=alignments.xml&amp;head_tag=alignment&amp;mode=1'>Add Database Now</a><BR/>";
    echo "<a href='../alignment/alignment_database.xml'>Alignment Database</a><BR/>";
    echo "<a href='../igrs/igr_database.xml'>IGR Database</a><BR/>";
    echo "<a href='../rdloci/rdloci_database.xml'>RD Loci Database</a><BR/>";
    
}
else if ($function == "stats") {
    $aligned_seqs = $_SESSION["aligned_seqs"];
    $stats = get_stats($aligned_seqs);
    display_stats($stats);
}
else if($function == "db_result") {
    $file_name = $_GET["file_name"];
    $aligned_seqs = load_clustal_file("alignments/".$file_name.".aln");
    $seqs = aligned_to_unaligned($aligned_seqs);
    $_SESSION["seqs"] = $seqs;
    $_SESSION["aligned_seqs"] = $aligned_seqs;
    display_alignment_horizontal($aligned_seqs,$font_size);
    display_report_form($file_name);
}
else {
    $seqs = get_sequences();
    $_SESSION["seqs"] = $seqs;
    $aligned_seqs = align_sequences($seqs, $file_name);
    $_SESSION["aligned_seqs"] = $aligned_seqs;
    display_alignment_horizontal($aligned_seqs,$font_size);
    display_report_form($file_name);
}