";
#################### Output data from Mysql into text files #########################
$q1 = "select filetype, name from bedfile where bedfile_id = $bedfile_id1";
$q2 = "select filetype, name from bedfile where bedfile_id = $bedfile_id2";
$row = mysql_fetch_row(mysql_query($q1));
$table1 = $row[0];
$name1 = $row[1];
//$filename1 = $row[1]; // need table1 name
$row = mysql_fetch_row(mysql_query($q2));
$table2 = $row[0];
$name2 = $row[1];
//$filename2 = $row[1]; // need table2 name
//print "Compared Files: (1)$filename1 (2)$filename2
";
if(!$table1 || !$table2) {
die("Invalid bedfile ID specified for compare().\n");
}
$temp = FILE_REPOSITORY_PATH . "/" . uniqid();
mkdir($temp);
// mysql user must have write perms
chmod($temp, 0777);
$filename1 = uniqid();
$filename2 = uniqid();
$db = getDB();
if($table1 == 'rawbed') {
//copy($db->getOne("select filepath from rawbed where bedfile_id = ?", $bedfile_id1), "$temp/$filename1");
$basefile = $db->getOne("select filepath from rawbed where bedfile_id = ?", $bedfile_id1);
`cut -f1-6 $basefile > $temp/$filename1`;
} else {
//$table1 = "${table1}_real";
$q3 = "select chrom,chromstart,chromend,name,score,strand from $table1 where bedfile_id = $bedfile_id1 order by chrom,chromstart into outfile '$temp/$filename1'";
//$q3 = "select chrom,chromstart,chromend,name,score,strand from ${table1}_real where bedfile_id = 1 order by chrom,chromstart into outfile '$temp/$filename1'";
mysql_query($q3) or die ("Error q3: $q3\n");
}
if($table2 == 'rawbed') {
//$table2 = "${table2}_real";
//copy($db->getOne("select filepath from rawbed where bedfile_id = ?", $bedfile_id2), "$temp/$filename2");
$basefile = $db->getOne("select filepath from rawbed where bedfile_id = ?", $bedfile_id2);
`cut -f1-6 $basefile > $temp/$filename2`;
} else {
$q4 = "select chrom,chromstart,chromend,name,score,strand from $table2 where bedfile_id = $bedfile_id2 order by chrom,chromstart into outfile '$temp/$filename2'";
//$q4 = "select chrom,chromstart,chromend,name,score,strand from ${table2}_real where bedfile_id = 2 order by chrom,chromstart into outfile '$temp/$filename2'";
mysql_query($q4) or die ("Error q4: $q4\n");
// prepend header onto file?
}
#################### Run bedtool #########################
//$temp = "temp/result.bed";
$resultfile = uniqid();
//$action = "/var/www/DASR_2011/BEDTools-Version-2.11.2/bin/intersectBed -wao -a $temp/$filename1 -b $temp/$filename2 > $temp/$resultfile"; // original overlapped file
$action = "/var/www/DASR_2011/BEDTools-Version-2.11.2/bin/intersectBed -wao -a $temp/$filename2 -b $temp/$filename1 > $temp/$resultfile"; // original overlapped file
system($action); // call BEDTools
############### Get cutoff processed file(combined columns)################
$random_number = genRandomString();
//print "
Please Keep Your Retrieval ID: $random_number
";
$new_file = "$temp/". uniqid() ."_combinedcolumns.txt"; //combined columns
overlaps_cut($new_file, "$temp/$resultfile", $overlaps);
###############overlap_bedfile(overlap interval)################
$new_file1 = "$temp/". uniqid() . "_overlapbedfile.txt"; // overlap_bedfile
$fh = fopen($new_file, "r") or exit("Unable to open $new_file!"); // read from an original overlapped file, $temp
$fh1 = fopen($new_file1, "w") or exit("Unable to write $new_file1!"); // write into a new overlapped file
while(!feof($fh)) {
$line = fgets($fh);
$chr = explode("\t", $line);
for($i = 1; $i <= sizeof($chr) - 1; $i++) {
if($chr[$i] == $chr[0]) {
$i += 1;
$low = max($chr[$i], $chr[1]); // low boundary of the overlap interval
$high = min($chr[$i + 1], $chr[2]); // high boundary of the overlap interval
fwrite($fh1, "$chr[0]\t$low\t$high\n");
}
}
}
fclose($fh);
fclose($fh1);
//system("chmod a+x 777 $new_file");
//system("chmod a+x 777 $new_file1");
##################ADDED BY G.Bonilla 06/13/2012 #################
################## insert results of overlap into summarybed table #############
/*
$err = '';
if(trim(`/usr/bin/wc -l $new_file1`) > RAWBED_THRESHOLD) {
#$db->query("insert into rawbed (bedfile_id, filepath) values (?,?)", array($bedfile_id1, $new_file1));
#$filetype = 'rawbed';
} else {
require_once 'load_bed.function.php';
$err = load_bed($bedfile_id1, $new_file1);
if(!$err) {
unlink($new_file1); // save space
$filetype = 'summarybed';
} else {
$db->query("update bedfile set descr = ? where bedfile_id = ?", array($err, $bedfile_id1));
#$db->query("insert into rawbed (bedfile_id, filepath) values (?,?)", array($bedfile_id1, $new_file1));
#$filetype = 'rawbed';
}
}
*/ ################----- end of added by G.B.------------------################################
#################### Plot Graphics #######################
$chromosome = chromosome_count($new_file);
$fmt_xaxis = join("|",array_keys($chromosome));
$fmt_yaxis = join(",",array_values($chromosome));
//cht (chart type), chd (data), and chs (chart size)
//print max(array_values($chromosome));
$chart1 = "https://chart.googleapis.com/chart?".
"cht=bvs".
"&chxt=x,y,y".
"&chm=N,000000,0,-1,11".
"&chxl=
0:|$fmt_xaxis|
2:|Overlap|counts|".
"&chxp=2,100,90".
"&chxs=2,0000FFFF".
"&chd=t:$fmt_yaxis".
"&chxr=1,0,".max(array_values($chromosome)).
"&chds=0,".max(array_values($chromosome)).
"&chbh=25,10,4".
"&chs=1000x200";
//print $chart1;
//print "Figure 1: Overlap-counts distribute on all Chromosome.";
$file1_percentage = get_percentage_array(chromosome_count($new_file), chromosome_count("$temp/$filename1"));
$file2_percentage = get_percentage_array(chromosome_count($new_file), chromosome_count("$temp/$filename2"));
$fmt_xaxis = join("|", array_keys($file1_percentage));
$fmt_yaxis_1 = join(",", array_values($file1_percentage));
$fmt_yaxis_2 = join(",", array_values($file2_percentage));
$chart2 = "https://chart.googleapis.com/chart?".
"cht=lc".
"&chxt=x,y,y".
"&chco=4D89F9,C6D9FD,".
"&chd=t:$fmt_yaxis_1|$fmt_yaxis_2".
"&chm=N,FF0000,0,-1,11,1.0|N,0000FF,1,-1,11,-1.0".
"&chdl=$name1|$name2". //fixme: use original names here, not temp names
"&chco=FF0000,0000FF".
"&chxl=
0:|$fmt_xaxis|
2:|Overlap|Per-Read|".
"&chxp=2,100,90".
"&chxs=2,0000FFFF".
//"&chxr=1,0,".max(array_values($file1_percentage)).
//"&chds=0,".max(array_values($file1_percentage)).
"&chxr=1,0,".max(max(array_values($file1_percentage)),max(array_values($file2_percentage))).
"&chds=0,".max(max(array_values($file1_percentage)),max(array_values($file2_percentage))).
"&chbh=25,15,4".
"&chs=1000x200";
//print $chart2;
//print "Figure 2: Overlaps-Per-Read(OPR) for $filename1 and $filename2.";
//print "Intuitively, a higher OPR curve indicates that two samples overlaps better.";
################# Statistics
#################### Remove the unnecessary files #######################
//system("rm $temp/$resultfile $temp/$filename2 $temp/$filename1");
//rrmdir($temp);
##################### Download #######################
//print "Format1-Combined Colummns:Download HERE";
//print "Format2-OverlapBedfile:Download HERE";
########################### Output Return #######################
//$path = $_SERVER['DOCUMENT_ROOT']."/DASR_2011/DASR_compare/";
#################### Statistics On a genome basis #######################
$total_overlaps = array_sum(array_values($chromosome));
$total_file1_percentage = round($total_overlaps/array_sum(array_values(chromosome_count("$temp/$filename1"))),4);
$total_file2_percentage = round($total_overlaps/array_sum(array_values(chromosome_count("$temp/$filename2"))),4);
$total_statistics =
array(
"Overlap_chr"=>$chromosome, // type :array
"Overlap_total"=>$total_overlaps, // type :int
"OPR_file1"=>$file1_percentage, // type :array
"OPR_file2"=>$file2_percentage, // type :array
"OPR_total_file1"=>$total_file1_percentage, //type :float
"OPR_total_file2"=>$total_file2_percentage //type :float
);
return array("overlap_bedfile" => $new_file1,
"overlap_combined_columns" => $new_file,
"overlaps_chart1" => $chart1,
"overlaps_chart2" => $chart2,
"temp" => $temp,
"total_statistics" => $total_statistics
);
}
###################### small functions #########################
function genRandomString() {
$length = 10;
$characters = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
$string = NULL;
for($p = 0; $p < $length; $p++) {
$string .= $characters[mt_rand(0, strlen($characters) - 1)];
}
return $string;
}
function overlaps_cut($new_file, $temp, $overlaps) {
$fh = fopen($temp, "r") or exit("Unable to open $temp!"); // read from an original overlapped file, $temp
$fh1 = fopen($new_file, "w") or exit("Unable to write $new_file!"); // write into a new overlapped file
while(!feof($fh)) {
$line = fgets($fh);
$chr = explode("\t",$line);
if((int)$chr[sizeof($chr) - 1] >= $overlaps) { // according to some criteria
//print "$chr $overlaps";
fwrite($fh1,$line);
}
}
fclose($fh);
fclose($fh1);
}
?>