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<?php |
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include_once("inc/settings.php"); |
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session_start(); |
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|
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function create_output_dir($job_name) { |
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$j = escapeshellcmd($job_name); |
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$output_dir = get_output_dir($job_name); |
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$cmd = "mkdir ".$output_dir; |
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exec($cmd); |
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} |
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|
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# writes two files |
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# 1: $job_name.fa - subsequence of $sequence from $seq_from to $seq_to |
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# 2: $job_name.full.fa - full $sequence with above subsequence in upper and rest in lower case |
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# fasta header of 1 is the job name |
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# fasta header of 2 is the subsequence index in a format like: >123-456 |
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# assumes that $sequence contains only amino acid characters and $seq_from and $seq_to are valid indices counting from 1 |
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function create_seq_files($job_name, $fullseq, $subseq, $seq_from, $seq_to) { |
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$seq_file = get_seq_file($job_name); |
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$full_seq_file = get_full_seq_file($job_name); |
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|
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// write subsequence |
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$fh = fopen($seq_file, 'w') or die("can't open file ".$seq_file); |
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fwrite($fh, ">".$job_name."\n"); |
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fwrite($fh, $subseq."\n"); |
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fclose($fh); |
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|
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// write full sequence |
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$fh = fopen($full_seq_file, 'w') or die("can't open file ".$full_seq_file); |
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fwrite($fh, ">".$seq_from.'-'.$seq_to."\n"); |
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fwrite($fh, $fullseq."\n"); |
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fclose($fh); |
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} |
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|
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function get_seq_file($job_name) { |
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$j = escapeshellcmd($job_name); |
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return $GLOBALS['server_root']."results/".$j."/".$j.".fa"; |
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} |
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|
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function get_full_seq_file($job_name) { |
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$j = escapeshellcmd($job_name); |
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return $GLOBALS['server_root']."results/".$j."/".$j.".full.fa"; |
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} |
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|
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function get_error_log_url($job_name) { |
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$j = escapeshellcmd($job_name); |
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return "results/".$j."/".$j.".err.log"; |
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} |
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|
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function get_error_log($job_name) { |
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$j = escapeshellcmd($job_name); |
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return $GLOBALS['server_root']."results/".$j."/".$j.".err.log"; |
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} |
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|
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function get_out_log($job_name) { |
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$j = escapeshellcmd($job_name); |
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return $GLOBALS['server_root']."results/".$j."/".$j.".out.log"; |
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} |
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|
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function get_ts_job_name($job_name) { |
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return 'TS-'.$job_name; |
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} |
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|
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function get_ts_lock_file($job_name) { |
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return get_result_file($job_name, ".TS.lock"); |
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} |
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|
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// writes a lock file indicating that template selection was started |
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function write_ts_lock_file($job_name) { |
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touch(get_ts_lock_file($job_name)); |
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} |
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|
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function run_template_selection($job_name) { |
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global $use_parallel_blast; |
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global $num_blast_cpus; |
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global $num_templates_in_report_file; |
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global $eval_cutoff_template_selection; |
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global $num_psiblast_iterations; |
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write_ts_lock_file($job_name); |
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$output_dir = get_output_dir($job_name); |
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$seq_file = get_seq_file($job_name); |
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$error_log = get_error_log($job_name); |
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$output_log = get_out_log($job_name); |
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|
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$n = $num_blast_cpus; |
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if($use_parallel_blast) { |
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# multi threaded blast search (default: 8 cpus) |
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$cmd = "qsub -pe threaded $n -V -N ".get_ts_job_name($job_name)." -e ".get_error_log($job_name)." -o ".get_out_log($job_name)." -q all.q /project/StruPPi/CASP8/scripts/templateSelection -i $seq_file -a $n -o $output_dir -j $num_psiblast_iterations -e $eval_cutoff_template_selection -x $num_templates_in_report_file"; |
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} else { |
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# single threaded blast search |
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$cmd = "qsub -V -N $job_name -e ".get_output_dir($job_name)." -o ".get_output_dir($job_name)." -q all.q /project/StruPPi/CASP8/scripts/templateSelection -i $seq_file -o $output_dir -j $num_psiblast_iterations -e $eval_cutoff_template_selection -x $num_templates_in_report_file"; |
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} |
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|
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$retval = 0; |
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system($cmd,$retval); |
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echo '<p></p>'; |
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#echo '<p>'.$cmd.'</p>'; |
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return $retval; |
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} |
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|
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if(!isset($_SESSION['job_name']) || !isset($_SESSION['sequence'])) { |
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header("Location: templates.php"); |
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} else { |
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$job_name = $_SESSION['job_name']; |
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$sequence = $_SESSION['sequence']; // full sequence in upper case |
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$seq_from = 1; |
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$seq_to = strlen($sequence); |
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if(array_key_exists('seqfrom',$_SESSION)) $seq_from = $_SESSION['seqfrom']; |
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if(array_key_exists('seqto',$_SESSION)) $seq_to = $_SESSION['seqto']; |
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|
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$subseq = substr($sequence, $seq_from - 1, $seq_to-$seq_from + 1); |
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$fullseq = strtolower(substr($sequence,0,$seq_from-1)).strtoupper($subseq).strtolower(substr($sequence,$seq_to)); |
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} |
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?> |
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> |
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<html xmlns="http://www.w3.org/1999/xhtml"> |
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|
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<head> |
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<title>Structure prediction server</title> |
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> |
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<link rel="stylesheet" type="text/css" href="css/default.css" /> |
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</head> |
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<body> |
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<?php include_once("inc/owl_header.inc.php") ?> |
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<h3>Template search</h3> |
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<?php |
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|
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echo "<p><b>Job name:</b> ".$job_name."</p>"; |
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|
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echo '<p><b>Target sequence: </b>'.$subseq.'</p>'; |
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|
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echo '<p><b>Position in full sequence: </b>'.$seq_from.'-'.$seq_to.'</p>'; |
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|
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// create output dir |
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create_output_dir($job_name); |
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|
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// write sequence to output dir |
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create_seq_files($job_name, $fullseq, $subseq, $seq_from, $seq_to); |
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|
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if(file_exists(get_ts_lock_file($job_name))) { |
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echo '<p>Job already submitted.</p>'; |
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} else { |
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// run templateSelection with output dir and sequence file |
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$result = run_template_selection($job_name); |
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if( $result != 0) { |
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echo '<p><font color="red">An error occured </font>(exit status='.$result.'). See the <a href="'.get_error_log_url($job_name).'">error log</a>.</p>'; |
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} |
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} |
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?> |
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|
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<div class="buttons"> |
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<a href="wait_for_templates.php?job_name=<? echo $job_name; ?>"><img src="images/eye.png" alt="" /> Check results</a> |
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</div> |
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|
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</body> |
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</html> |
