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ktsirig

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About ktsirig

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  1. Hi, thanks for your answer... My problem is that I have absolutely no idea how to do this, can you point me to some place?
  2. Hi, I have an input form for a user to submit some input and then this input is processed by a Perl script, which is called through the PHP index page... My problem is that this external script takes usually more than 2-3 minutes so there is a risk of the page to hang. How can I modify my PHP page to stay in index.php, but periodically refresh it so, when the perl command is done, it then outputs the results. Here is the index page (the refresh I wrote on top did not work. <?php $max_seqs = 1000; $page = $_SERVER['PHP_SELF']; $sec = "10"; header("Refresh: $sec; url=$page"); ?> <html> <head> <style> body { font-family: arial; color: #003965; font-size: 14px; } textarea { width: 620px; height: 120px; font-family: courier; } .whole { width: 1000px; border-collapse: collapse; margin-top:20px; margin-bottom:20px; text-align: center; background-color: #e8e8e8; font-size: 12px; } .browse_cell { background:#d8dada; font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 13px; padding: 3; border-spacing: 2; text-align: center; font-weight: bold; color:#424d5d; } .browse_cell_change1 { background:#BFBFF6; font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 11px; padding: 2; } .browse_cell_change2 { background:#D9D9D9; font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 11px; padding: 2; border-spacing:4px; } .headcell { font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 16px; font-weight:bold; line-height: 15px; text-align: center; color: #000144; } </style> </head> <body> <?php if( isset ( $_POST['sequence'] )) #run part { function readSeqs($text) { if( !preg_match( '/^>/m', $text ) ) return readSeqs( ">\n$text" ); $seqs = array(); $text = preg_replace( '/[\n\r]+/', "\n", $text ); preg_match_all( '/^>([^\n]*)\n([^>]*)/ms', $text, $matches ); foreach( $matches[1] as $k=>$name1 ) { $seqs_number++; $seq = $matches[2][$k]; $name1 = trim($name1); $name=substr($name1, 0, 50); #keep only the first 40 characters (if the name is longer) $name=preg_replace('/\s+/', ' ', $name); $name=preg_replace('/[\|\s\/\\\%\*&\#\@\(\)\[\]\$\^\!]/', '_', $name); $seq = preg_replace( '/\s+/', '', $seq ); $seqs[] = array( 'name'=>$name, 'seq'=>$seq ); } return $seqs; } $uniq_number = uniqid(); $input_folder = './tmp_files/myfolder_'.$uniq_number; mkdir($input_folder); $input_file = $input_folder.'/'.'input_seqs'; $seqs = readSeqs($_POST['sequence']); $run_mode = $_POST['mode']; $signal=''; $phmms=''; if($_POST[sp_pred] == 'on') { $signal = $_POST['sp_pred']; } else { $signal = 'off'; } if($_POST['pfams'] == 'on') { $phmms = $_POST['pfams']; } else { $phmms = 'off'; } $seqs_number = count($seqs); $prior_info1 = $_POST['prior']; if (preg_match('/Example/', $prior_info1)) { $prior_info='--'; $prior_info_final='NO_INFO'; } else { $prior_info=$prior_info1; $prior_info_final=str_replace(';', 'A', $prior_info); } if( $seqs_number == 0 ) { echo "<em>You did not submit any sequences.</em>"; } elseif( $seqs_number > $max_seqs ) { echo "<em>You can input no more than $max_seqs sequences at a time.</em>"; } elseif ( $seqs_number > 1 and $seqs_number <= $max_seqs ) { $input = ''; foreach($seqs as $v) #create input file for run { $input.= ">".$v['name']."\n".$v['seq']."\n"; } #write each FASTA seq in input file file_put_contents( $input_file, $input ); #(if we will allow >1 proteins) #echo "perl Whole_Program.pl $input_folder $seqs_number $prior_info_final $run_mode $signal $phmms<br>"; exec ("perl Whole_Program.pl $input_folder $seqs_number $prior_info_final $run_mode $signal $phmms", $res_total, $ret); if($ret==0) { $text_file = $input_file.'.txt_res'; $zip_file = 'tmp_files/'.$uniq_number.'.tgz'; echo "<table class=\"whole\">\n"; echo "<tbody>\n"; echo "<tr><td class=\"headcell\" align=\"right\" colspan=\"7\"><br>Results<br><br></td></tr>\n"; echo "<tr>\n"; echo "<td width=\"14%\" class=\"browse_cell\">Entry</td>\n". "<td width=\"12%\" class=\"browse_cell\">Length</td>\n". "<td width=\"14%\" class=\"browse_cell\">Signal peptide</td>\n". "<td width=\"14%\" class=\"browse_cell\">β-score</td>\n". "<td width=\"38%\" class=\"browse_cell\">OMPdb family</td>\n". "<td width=\"14%\" class=\"browse_cell\">#TM</td>\n". "<td width=\"12%\" class=\"browse_cell\">Topology image</td>\n"; echo "</tr>\n"; foreach ($res_total as $line_entry) { $counter++; if ($counter % 2) {$colour_class="browse_cell_change1";} else {$colour_class="browse_cell_change2";} $all_data = preg_split("/\t/", $line_entry); $id=$all_data[0]; $seq_len=$all_data[1]; $signal=$all_data[2]; $score=$all_data[3]; $family_name=$all_data[4]; $family_number=$families_array[$family_name]; $tm_num=$all_data[5]; if($tm_num==0) {$tm_num='--';} $topo_img_link=$all_data[6]; echo "<tr>\n"; echo "<td width=\"14%\" align=\"left\" class=\"".$colour_class."\">".$id."</td>\n". "<td width=\"12%\" class=\"".$colour_class."\">".$seq_len."</td>\n". "<td width=\"14%\" class=\"".$colour_class."\">".$signal."</td>\n". "<td width=\"14%\" class=\"".$colour_class."\">".$score."</td>\n". "<td width=\"38%\" align=\"left\" class=\"".$colour_class."\">"; if($family_name == "--") { echo "$family_name</td>\n"; } else { echo "<a target=\"_blank\" href=\"http://www.ompdb.org/OMPdb/view_family.php?fam_id=".$family_number."\">". $family_name."</a></td>\n"; } echo "<td width=\"14%\" class=\"".$colour_class."\">".$tm_num."</td>\n"; if($topo_img_link=='--') { echo "<td width=\"12%\" class=\"".$colour_class."\">--</td>\n"; } else { echo "<td width=\"12%\" class=\"".$colour_class."\"><a target=\"_blank\" href=\"".$topo_img_link."\"> Download</a></td>\n"; } echo "</tr>\n"; } echo "</tbody></table>\n"; } else { echo "<br /><br />Program error!"; } } echo "<br /><a target=\"_blank\" href=\"".$text_file."\">Download</a> results in plain text format\n"; echo "<br /><a target=\"_blank\" href=\"".$zip_file."\">Download</a> all files related to this submission as a tarball\n"; echo "<br /><br /><a href=\"index.php\">Run again</a><br />"; } else #index initial page { echo "Please paste up one or more ". " - formatted sequences in the textarea below: <br /><br />\n"; echo "<form method=post name=\"seq_form\">". "<textarea name=\"sequence\"></textarea> <br /><br /> Select mode: <input type=\"radio\" name=\"mode\" value=\"1\" checked /> MSA-version (1 sequence) <input type=\"radio\" name=\"mode\" value=\"2\" /> Single-sequence version (up to $max_seqs sequences) <br /><br /> Run signal-peptide prediction using <a target=\"_blank\" href=\"http://www.compgen.org/tools/PRED-TAT/\">PRED-TAT</a>: <input type=\"checkbox\" name=\"sp_pred\" checked> <br /><br /> Use library in prediction: <input type=\"checkbox\" name=\"pfams\" checked> <br /><br /> Prior information (constrained prediction): <input type=\"text\" name=\"prior\" size=\"33\" style=\"color:#888;\" value=\"Example: I:1-15;M:20-25;O:30-30\" onfocus=\"inputFocus(this)\" onblur=\"inputBlur(this)\" /> <br /><br /> <input type=\"submit\" value=\"Run prediction\" /> <input type=\"reset\" value=\"Clear fields\" /> <input type=\"button\" value=\"Generate sample input\" onclick=\"example_fill();\"> </form>"; echo "<br /><hr>"; } ?> </body> </html>
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