Chromatin Folding

$val) { echo $val."

";}} } ################################################################################################################################################################################ function counter() { ##This function opperates the counter and cleans-up the sessions directory global $SID, $count, $sesspath; if ($SID == 0){ ##Take the hits from the file $count $hits = file($count); ##Increment it by one $hits[0] ++; ##write the new number to the file $count $fp = fopen($count , "w"); fputs($fp , "$hits[0]"); fclose($fp); $SID = $hits[0]; ##Make directory for the new session mkdir("$sesspath$SID", 0777); } ##The variable SIDmTen controls how many full session directories are kept and how many are archived $SIDmTen = $SID - 10; $dir = "$sesspath/$SIDmTen"; $directory = escapeshellarg($dir); exec("rm -rf $directory"); } ##This function creates a temporary file with an unverified sequence in it. ## This file is then used by makeconfig() as to verify that all characters are valid. ## This was done in this manner as to allow makeconfig work with both form data and uploaded data. ######################################################################################## function makeconfig() { global $confin, $directions, $errors, $K, $linker, $MMTV, $nuclength, $nss, $nssarr, $numnuc,$reqtypenss, $requpseq, $seqscanfile, $seqinlength, $sesspath, $seqin, $SID, $validseq, $X, $X0; ## This function writes the sequence file and confirms that all user input data is valid, ## then writes the confin file ## make global variables $seqinfile = "$sesspath$SID/seqin.txt"; $uploadfile = "$sesspath/$SID/uploaded.txt"; #Read nuclength from $X file $fh = fopen($X, 'r'); $nuclength = fread($fh, 5); fclose($fh); $subseq = substr($seqin, 0, 15); $subdirections = substr($directions, 0, 15); if ($subseq == $subdirections){ $seqin = $MMTV;} if ($requpseq == 1 ) { uploader(); $fh0 = fopen($uploadfile, 'r'); $seqin = fread($fh0, filesize($uploadfile)); fclose($fh0); } if (preg_match('/[^A,T,G,C,\s]/i', $seqin)) { ##if not A, T, G, C's add an error to the error array and re-print the form $errors['seqin'] = "ERROR:your sequence must have only: a, t, g, c, \n A, T, G, C \n or spaces."; $validseq = FALSE; ##otherwise make $validseq true so form can be reprinted } else {$validseq = TRUE;} $seq4prog = trim(chunk_split(strtoupper(preg_replace('/[^A,T,G,C]/i','', $seqin)), 1, "\n")); $seqinlength = (strlen($seq4prog)+1)/2; $fp = fopen($seqinfile, 'w+'); fwrite($fp, $seq4prog ); fclose($fp); if ($reqtypenss == 1) { $eqconfin = "$X0\n$sesspath$SID/seqin.txt\n$sesspath$SID/eq.out.par\n"; $fn = "$sesspath/$SID/eq.conf.in"; $fp = fopen($fn, 'w+'); fwrite($fp, $eqconfin ); fclose($fp); $seqscandat = "$X0\n$X\n$K\n$sesspath$SID/seqin.txt\n$sesspath$SID/E.out"; $seqscanfile = "$sesspath$SID/seqscan.txt"; $fp = fopen($seqscanfile, 'w+'); fwrite($fp, $seqscandat ); fclose($fp); #calc numnuc ##trim whitespaces $nssarr = split("[\n\r\t ,]+", trim($nss)); $numnuc = count($nssarr); $nss = implode("\n", $nssarr); $confin = "$X0\n$X\n$sesspath$SID/seqin.txt\n$nss\n-$numnuc\n$sesspath$SID/wdna.par\n"; } elseif($reqtypenss == 0) { ##CAUTION ##adding text to the string $confinE seems to affect the fortran code ### changing the helical parameters, energy values and so forth. ## numnuc can be < 0 => a shift ; just report as negative number add 2 b/c icm program error ## >0 && < 1 => a percentage of max; must be converted to integer ## >= 1 a number of nucleosomes if ($numnuc < 0 ) { $numnuc = floor($numnuc) + 2 ; } elseif ($numnuc < 1 ) { $numnuc = floor($numnuc*$seqinlength*1.0/($nuclength+$linker)); } $confin = "$X0\n$X\n$K\n$sesspath$SID/seqin.txt\n$sesspath$SID/eq.out.par\n$sesspath$SID/E.dat\n$numnuc\n$linker\n"; } #write confin $fp = fopen("$sesspath$SID/confin.txt", 'w+'); fwrite($fp, $confin ); fclose($fp); } ######################################################################################## function uploader() { ##make global variables global $SID, $sesspath; //Сheck that we have a file if((!empty($_FILES["uploadedfile"])) && ($_FILES['uploaded_file']['error'] == 0)) { //Check if the file is txt and it's size is less than 500Kb $filename = basename($_FILES['uploadedfile']['name']); $ext = substr($filename, strrpos($filename, '.') + 1); if (($ext == "txt") && ($_FILES["uploadedfile"]) && ($_FILES["uploadedfile"]["size"] < 500000)) { //Determine the path to which we want to save this file $newname = "$sesspath$SID/" . "uploaded.txt"; //Check if the file with the same name is already exists on the server if (!file_exists($newname)) { //move the uploaded file to uploads/ if ((move_uploaded_file($_FILES['uploadedfile']['tmp_name'],$newname))) { $requpseq = 1; } else { echo "Error: A problem occurred during file upload!"; } } else { echo "Error: File ".$_FILES["uploadedfile"]["name"]." already exists; please save the file with another name and try again."; } } else { echo "Error: Only .txt files under 500Kb are accepted for upload"; } } else { echo "Error: No file uploaded"; } } ######################################################################################## ## This function opens the nss file and confirms that all user input data is valid. function pc_validate_nss() { global $errors, $linker, $nss, $nssarr, $nuclength, $numnuc, $seqinlength, $sesspath, $SID, $validnss, $X; #$nss1 = explode("/n", $nss); ##verify entry contains only numerical entries if (preg_match('/[^0-9,\s]/i', $_POST['nss']) == TRUE){ $nsscond1 = FALSE; $errors['nss'] = "ERROR: nucleosome start sites are numerical values separated by spaces"; }else{ ##open nucleosome files and obtain the length of the nucleosome selected. $fh = fopen($X, 'r'); $nuclength = fread($fh, 5); fclose($fh); if ($nss == ""){ $nsscond2 = FALSE; $errors['nssempty'] = "If the energy function is to be bypassed at least one nucleosome start site must be specified.";} else { sort($nssarr, SORT_NUMERIC); ##delete duplicate values $nss = array_unique($nssarr); $last = end($nss); $maxnss = $seqinlength - $nuclength; if ($last > $maxnss) { if ($seqinlength < $nuclength) { $nsscond3 = FALSE; $errors['nssseq'] = "Each selected nucleosome is $nuclength" . "bp in length. \nPlease specify a sequence that is greater than $nuclength" . "bp long."; } elseif ($seqinlength > $nuclength) { $nsscond4 = FALSE; $errors['nssend'] = "You have requested a nucleosome start site that is less than \n $nuclength from the end of your sequence. The last nucleosome start \n site for this sequence must be less than $maxnss"; } } $zeros = range(1, $seqinlength); ## from [0] to [n-1] in the array $nss subtract the value [i+1] from the value [i] $i=0; while($i < count($nss) -1) { $diff = $nss[$i+1] - $nss[$i]; $i++; ## if $diff is less than the $nuclength condition is false, otherwise condition is true if ($diff < $nuclength ) { $tooclose[] = $nss[$i-1]; $tooclose[] = $nss[$i]; $gtnuclength = false; $tooclose = join(', ', array_unique($tooclose)); $errors['nssclose'] = "Please fix your nucleosome start sites as to insure there \n are at least $nuclength bp between each nucleosome. The nucleosomes \n at: " . $tooclose . " are less than $nuclength bp apart."; $nsscond5 = FALSE; }else $gtnuclength = true; } }} if($nsscond1 = FALSE || $nsscond2 = FALSE || $nsscond3 = FALSE || $nsscond4 = FALSE || $nsscond5 = FALSE){$validnss = "";} else{$validnss = TRUE; } } ######################################################################################## ######################################################################################## ##These functions are used to begin/end *MOST* html files created by the program. This is one area that could be cleaned up significantly and made more robust as to make the program run faster and smoother. function htmlbegin($script, $css){ echo << $script $css Chromatin Folding HEAD; } function htmlend(){ echo " ";} ######################################################################################## ######################################################################################## ##This function prints the main form that the user uses to imput data. function print_form($seqin, $K, $X, $X0){ global $directions, $dirK, $dirX, $dirX0, $dirSeq, $Energy, $errors, $nssintype_1, $reqtypenss, $requestnss, $requpseq, $SID, $webdirSeq; ##This function makes the menus for K, X, XO and the sample sequences. function menu($indir, $outdir, $ext, $selectname){ $files = array(); $handle = opendir($indir); while($filename = readdir($handle)) {if ( substr( $filename, -4 ) == "$ext" ) { $files[] = $filename;}} closedir($handle); sort( $files ); // Output results foreach( $files AS $name ) { echo " \n";} } ##This function makes the Go/Reset buttons function goreset ($type, $value, $onclick){ echo << GORESET; } ##Determine if directions or the user's sequence should be printed in the textbox if (isset($_POST['seqin'])) {$seqin = $_POST['seqin'];} else {$seqin = "$directions";} ##Define whether or not the user will see the text box to insert NSS's, or if they will see a button requesting to the text box. The function is similiar to the seqtype() function ##These are the var that prints the default button $nssintype0 = ''; $requestnss0 = ""; ##These are the var for the the upload button $nssintype1 = ' '; $requestnss1 =''; if ($reqtypenss == 1) { $requestnss = $requestnss1; $Energy = FALSE; if ($requpseq == 1) { $nssin_type = $nssintype1; $nssintype_1 = $nssintype1; } elseif ($requpseq == 0) { $nssin_type = ""; $nssintype_1 = $nssintype1; $requestnss = $requestnss1;}} elseif ($reqtypenss == 0) { $nssin_type = $nssintype0; $requestnss = $requestnss0; $Energy = TRUE;} ##This function defines whether or not the user will see the button to browse their file system for a sequence file, or if they will see a button requesting to upload a file. $seqintype0=''; $requestseq0 = " "; $seqform0 = "

"; $seqintype1 = ' Choose a DNA sequence to upload:

'; $requestseq1 = ""; $seqform1 = ""; if ($requpseq == 1) { $seqin_type = $seqintype1; $requestseq = $requestseq1; $seqform = $seqform1;} elseif ($requpseq == 0) { $seqin_type = $seqintype0; $requestseq = $requestseq0; $seqform = $seqform0;} ##Begin printing form htmlbegin("", ""); echo <<

STYLEINFO; errors(); echo <<
Interactive Chromatin Folding
(I see 'em.)

	$seqform HEADERINFO; ###$requestseq ##echo << ## ## ##SAMPLE; ##menu($dirSeq, $webdirSeq, ".txt", "Seq"); if ($Energy == TRUE){ echo " Energy Options: $requestnss E_nuc = ½ K(X - X₀)² " ; echo " "; ##K value menu echo "K = "; ##X value menu echo "X = "; ##X0 value menu echo "X₀ = "; echo " " ; } else { echo " Conformation: " ; echo " "; ##X value menu echo "Nucleosomes = "; ##X0 value menu echo "Linker = "; echo " " ; } if ($reqtypenss == 0){ echo << Occupancy: Nucleosomes: number: n > 1 : number nucleosomes n < 1 : percentage of max n = 0 : constant nucleosome spacing n < 0 : constant spacing + shift Linker: length: OCCUPANCY; } elseif ( $reqtypenss == 1) { echo << Positions: $nssintype_1 OCCUPANCY; } goreset("submit", "Go", " "); goreset("button", "Reset", "ONCLICK=\"window.location.href='$_SERVER[PHP_SELF]'\" "); echo <<

$seqform

HEADERINFO; ###$requestseq ##echo << ##
## ##SAMPLE; ##menu($dirSeq, $webdirSeq, ".txt", "Seq"); if ($Energy == TRUE){ echo " Energy Options: $requestnss

E_nuc = ½ K(X - X₀)²
" ; echo "
"; ##K value menu echo "K =

"; ##X value menu echo "X =

"; ##X0 value menu echo "X₀ =

"; echo "
" ; } else { echo " Conformation:
" ; echo "
"; ##X value menu echo "Nucleosomes =

"; ##X0 value menu echo "Linker =

"; echo "
" ; } if ($reqtypenss == 0){ echo << Occupancy:

Nucleosomes:
number:
n > 1 : number nucleosomes
n < 1 : percentage of max
n = 0 : constant nucleosome spacing
n < 0 : constant spacing + shift

Linker:
length:

OCCUPANCY; } elseif ( $reqtypenss == 1) { echo << Positions:
$nssintype_1
OCCUPANCY; } goreset("submit", "Go", " "); goreset("button", "Reset", "ONCLICK=\"window.location.href='$_SERVER[PHP_SELF]'\" "); echo <<

Try one of our samples here: $requestseq ENDFORM; htmlend(); } ######################################################################################## ######################################################################################## ##This function prints all output from the form. function print_output() { global $betaformxyz, $chromatinxyz, $cssout, $jmolscript, $seqin, $SID, $webdir, $sesspath, $progDIR ; htmlbegin($jmolscript, $cssout); echo <<

Click images for larger view

Shift

Tilt

Java may take a moment to load.

Please be patient.

Click for a larger view

Save Energy data

Free DNA

Chromatin

END; passthru("cd $sesspath$SID ; $progDIR/xyz2dists "); echo <<

Right Click Jmol image for options

Download Java

Slide

Roll

Rise

Twist

END; } ### TcB 5/5 cleaned up html manually from top to this point ### NOTE that only nss seems to work correctly at this point ################################################################################################################################################################################ function jmol_html($infile, $outfile) { global $sesspath, $SID; $string = << Bishop Lab - END; $fn = "$sesspath$SID/$outfile"; $fp = fopen($fn, 'w+'); {fwrite($fp, $string );} fclose($fp); } ################################################################################################################################################################################ function conditionsmet(){ print_output(); jmol_html("eq.out.xyz", "betaform.html"); jmol_html("wdna.occ.xyz", "chromatin.html"); } ################################################################################################################################################################################ ##CALL FUNCTIONS AS NEEDED counter(); if (isset($_POST['stage']) && ('process' == $_POST['stage'])) { if (empty($errors)) { makeconfig(); if ($reqtypenss == 1) { pc_validate_nss(); if (empty($errors)) { if(($validseq = TRUE) && ($validnss = TRUE)){ exec("cd $sesspath$SID ; cat $sesspath$SID/confin.txt | $usrbin/fold-conf"); exec("cd $sesspath$SID ;cat $seqscanfile | $usrbin/seq-scan"); exec("cd $sesspath$SID ; cat $sesspath$SID/eq.conf.in | $usrbin/eq-conf"); exec("cd $sesspath$SID ; $progDIR/nss.awk E.out $nuclength > $sesspath$SID/wdna.dat"); exec("cd $sesspath$SID ; $progDIR/make-xyz-from-par.tcsh $numnuc "); exec("awk < $sesspath$SID/wdna.dat '{ print $1, $3 }' > $sesspath$SID/wdnagraph.dat"); passthru("cd $sesspath$SID ; /home/www/htdocs/wdna/prog/makepng.tcsh"); print_output(); jmol_html("eq.out.xyz", "betaform.html"); jmol_html("wdna.occ.xyz", "chromatin.html"); } } else { print_form(); } } elseif ($reqtypenss == 0){ if (empty($errors)) { if (TRUE == $validseq) { exec("cd $sesspath$SID ; cat $sesspath$SID/confin.txt | $usrbin/icm"); exec("cd $sesspath$SID ; $progDIR/make-xyz-from-par.tcsh $numnuc "); exec("awk '{print $1, $3}' $sesspath$SID/wdna.dat > $sesspath$SID/wdnagraph.dat"); exec("gracebat -autoscale y -hardcopy -hdevice PNG -printfile $sesspath$SID/E.png -fixed 400 320 -nxy $sesspath$SID/wdna.dat"); exec("cd $sesspath$SID ; $progDIR/makepng.tcsh"); if (empty($errors)) { conditionsmet(); }} else { print_form(); } } elseif (FALSE == $validseq) {print_form();} } } else {print_form();} } else {print_form();} ?>

STYLEINFO; errors(); echo << Interactive Chromatin Folding (I see 'em.)

"; ##K value menu echo "K = "; menu($dirK, $dirK, ".dat", "K"); echo " "; ##X value menu echo "X = "; menu($dirX, $dirX, ".par", "X"); echo " "; ##X0 value menu echo "X0 = "; menu($dirX0, $dirX0, ".par", "X0"); echo " "; echo "

"; ##X value menu echo "Nucleosomes = "; menu($dirX, $dirX, ".par", "X"); echo " "; ##X0 value menu echo "Linker = "; menu($dirX0, $dirX0, ".par", "X0"); echo " "; echo "

Nucleosomes: number: n > 1 : number nucleosomes n < 1 : percentage of max n = 0 : constant nucleosome spacing n < 0 : constant spacing + shift Linker: length:

OCCUPANCY; } elseif ( $reqtypenss == 1) { echo << Positions: $nssintype_1 OCCUPANCY; } goreset("submit", "Go", " "); goreset("button", "Reset", "ONCLICK=\"window.location.href='$_SERVER[PHP_SELF]'\" "); echo <<