#!/usr/local/bin/perl -w #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ # Program : CreateBiosapRun.cgi # Author : Michael Johnson # $Id$ # # Description : This CGI program allows users to generate biosap # parameter files in unique directories (under a # directory), based on input they provide through # a web interface. # # SBEAMS is Copyright (C) 2000-2005 Institute for Systems Biology # This program is governed by the terms of the GNU General Public License (GPL) # version 2 as published by the Free Software Foundation. It is provided # WITHOUT ANY WARRANTY. See the full description of GPL terms in the # LICENSE file distributed with this software. # #----------------------------------------------------------------------- ############################################################################### # Set up all needed modules and objects ############################################################################### use strict; use Getopt::Long; use FindBin; use POSIX qw(strftime); use POSIX qw(:sys_wait_h); use lib qw (../../lib/perl); use vars qw ($q $tm $tm_rng $o_conc $s_conc $blast_lib $same_as_lib $mn_len $mx_len $mx_selfcomp $init_offset $step $dist $ftrs $featurama_lib $dirstr $pol_at $pol_gc $win_sz $win_at $win_gc $action $comments $PROG_NAME $dbh $sbeams $sbeamsMOD $current_username $USAGE %OPTIONS $VERBOSE $QUIET $DEBUG); use DBI; #use CGI; use CGI::Carp qw(fatalsToBrowser croak); use SBEAMS::Connection qw($q); use SBEAMS::Connection::Settings; use SBEAMS::Connection::Tables; use SBEAMS::Biosap; use SBEAMS::Biosap::Settings; use SBEAMS::Biosap::Tables; $sbeams = new SBEAMS::Connection; $sbeamsMOD = new SBEAMS::Biosap; $sbeamsMOD->setSBEAMS($sbeams); $sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR); #$q = new CGI; ############################################################################### # Set program name and usage banner for command like use ############################################################################### $PROG_NAME = $FindBin::Script; $USAGE = <Authenticate( #connect_read_only=>1, #allow_anonymous_access=>1, #permitted_work_groups_ref=>['Proteomics_user','Proteomics_admin'], )); #### Read in the default input parameters my %parameters; my $n_params_found = $sbeams->parse_input_parameters( q=>$q,parameters_ref=>\%parameters); #$sbeams->printDebuggingInfo($q); #### Decide what action to take based on information so far $sbeamsMOD->printPageHeader(); if ($parameters{action} eq "Submit to BioSap") { process_request(ref_parameters=>\%parameters, testonly=>0); }elsif ($parameters{action} eq "Test Run Featurama") { process_request(ref_parameters=>\%parameters, testonly=>1); }else { print_javascript(); create_request_form(ref_parameters=>\%parameters); } $sbeamsMOD->printPageFooter(); } # end main ############################################################################### # print_javascript ############################################################################## sub print_javascript { print qq~ ~; return 1; } ############################################################################### # Process Request ############################################################################### sub process_request { my %args = @_; my $SUB_NAME = "process_request"; #### Process the arguments list my $ref_parameters = $args{'ref_parameters'} || die "ERROR[$SUB_NAME]: ref_parameters not passed"; my $testonly = $args{'testonly'}; #### If the parameters are okay, then create the necessary files my ($ok, $ref_parameters) = verify_parameters(ref_parameters=>$ref_parameters); if ($ok == 1) { my $output_dir = make_output_dir (testonly=>$testonly); write_parameters_files(ref_parameters=>$ref_parameters, output_dir=>$output_dir); if ($testonly==1){run_featurama(output_dir=>$output_dir);} else { print qq~ You have successfully subbmitted a job to BIOSAP
Your job will be processed in the order received. You can see the log file of your job by clicking on the link below:

Well, theres no link yet, but paste this into a unix window:

cd $output_dir
if ( -e $output_dir ) tail -f blast.out



~; } } create_request_form(ref_parameters=>$ref_parameters); return; } # end process_request ############################################################################### # run_featurama ############################################################################### sub run_featurama { my %args = @_; my $SUB_NAME = "run_featurama"; #### Process the argument list my $output_dir = $args{'output_dir'} || die "ERROR[$SUB_NAME]: output_dir not passed!\n"; #### Define standard variables my $featurama_location = "/net/db/projects/BioSap/src/biosap/featurama/src"; my $featurama_params = "$output_dir/featurama.params"; my ($start_hour,$start_min,$start_sec) = ((localtime)[2],(localtime)[1],(localtime)[0]); $| = 1; print "
\n";
  system "$featurama_location/featurama $featurama_params 2>&1" 
      || croak "Couldn't run featurama : $!";
  print "
\n";
  system "/bin/rm -fr $output_dir"
      || croak "Couldn't formatdb: $!";

  my ($finish_hour,$finish_min,$finish_sec) = ((localtime)[2],(localtime)[1],(localtime)[0]);

  print qq ~
    

    

      
      
      Featurama Test Run is Done !

      Started at $start_hour:$start_min:$start_sec

      Completed at $finish_hour:$finish_min:$finish_sec

      
      		
    

    

    ~;
}
###############################################################################
# write_parameters_files
###############################################################################
sub write_parameters_files {
  my %args = @_;
  my $SUB_NAME = "write_parameters_files";

  #### Process the arguments list
  my $ref_parameters = $args{'ref_parameters'}
  || die "ref_parameters not passed\n";
  my %parameters = %{$ref_parameters};
  my $output_dir = $args{'output_dir'}
  || die "output_dir not passed\n";
  my ($sql,@rows);

  #### write Comments file
  open (COMMENTS, ">$output_dir/comments")
      || croak "ERROR[$SUB_NAME]: could not create comments file\n";
  if ($parameters{'comments'}) {
    print (COMMENTS $parameters{'comments'});
  }else {
    print (COMMENTS "No comments were submitted\n");
  }
  close (COMMENTS);
  

  #### write Featurama parameters file
  open (FEATURAMA, ">$output_dir/featurama.params")
	|| croak "ERROR[$SUB_NAME]: could not create featurama parameters file\n";
	my $user = $sbeams->getCurrent_username();
  my $featurama_params =  "user_name=$user\n";

  my $bs_id = $parameters{'featuramalib'};
  $sql = qq~
      SELECT set_path
        FROM $TBBS_BIOSEQUENCE_SET
       WHERE biosequence_set_id = '$bs_id'
         AND record_status != 'D'
	 ~;
  @rows = $sbeams->selectOneColumn($sql);
  my $biosequence_set = $rows[0];

  $featurama_params .=  qq~gene_library=$biosequence_set
output_directory=$output_dir
melting_temp=$parameters{'meltTemp'}
melting_temp_range=$parameters{'meltTempRange'}
minimum_length=$parameters{'minLen'}
maximum_length=$parameters{'maxLen'}
maximum_selfcomp=$parameters{'maxSelfComp'}
step_size=$parameters{'stepSize'}
maximum_3prime_distance=$parameters{'max3PrimeDist'}
initial_3prime_offset=$parameters{'initOffset'}
maximum_features=$parameters{'maxReporters'}
maximum_polyAT_length=$parameters{'maxPolyAT'}
maximum_polyGC_length=$parameters{'maxPolyGC'}
content_window_size=$parameters{'windowSize'}
maximum_windowAT_content=$parameters{'maxATinWindow'}
maximum_windowGC_content=$parameters{'maxGCinWindow'}
oligo_concentration_mMol=$parameters{'oligoConc'}
salt_concentration_mMol=$parameters{'saltConc'}~;
#	print "
$featurama_params
";
  print FEATURAMA $featurama_params;
  close(FEATURAMA) || print "WARNING[$SUB_NAME]: featurama params file did not close nicely!
";
  print "File ".$output_dir."/featurama.params created.
";
  
  #### write BLAST parameters file
  open (BLAST, ">$output_dir/blast.params")
      || croak "ERROR[$SUB_NAME]: could not create BLAST parameters file\n";
  my $blast_lib = $parameters{'blastlib'};
  $sql = qq~
      SELECT set_path
        FROM $TBBS_BIOSEQUENCE_SET
       WHERE biosequence_set_id = '$blast_lib'
         AND record_status != 'D'
	 ~;
  my @blast_lib_id = $sbeams->selectOneColumn($sql);

  print BLAST qq~blast_library=$blast_lib_id[0]
expect_value=1
~;
  close (BLAST) || print "WARNING[$SUB_NAME]: blast params file did not close nicely!
";
  print "File ".$output_dir."/blast.params created.
";
  
  return;

} # end write_parameters_files

###############################################################################
# make_output_dir
###############################################################################
sub make_output_dir {
  my %args = @_;
  my $SUB_NAME = "make_output_dir";

  #### Process the arguments list
  my $testonly = $args{'testonly'};
  my $unique_dir = 0;
#	my $output_dir = "/net/techdev/biosap_ext"; # for MySQL site
  my $output_dir = "/net/techdev/biosap/"; # for ISB-internal site
  ($testonly == 1) ? ($output_dir .= "tmp/") : ($output_dir .= "data/");

  #### Create an output directory.  Make sure it's unique
  for (my $i=0; $i<10 && $unique_dir==0; $i++) {
    my ($sec,$min,$hour,$mday,$mon,$year) = localtime(time);
    $output_dir .= strftime("%Y%m%d.%H%M%S",$sec,$min,$hour,$mday,$mon,$year);
    if (-e $output_dir) {
      print "WARNING[$SUB_NAME]: ".$output_dir." is not unique. This is attempt ".
	  ($i+1)." of 10
\n";
      sleep 5;
    }else {
      $unique_dir = 1;
      mkdir ($output_dir) || croak "ERROR[$SUB_NAME]: directory ".
	  $output_dir."could not be created.\n".$!;
      chmod (0777, $output_dir) || croak "ERROR[$SUB_NAME]: could not change".
	  "permissions for directory ".$output_dir."\n";
      print "Directory ".$output_dir." created successfully
";
    }
  }
  return $output_dir;

} # end process_request

###############################################################################
# Create Request Form
###############################################################################
sub create_request_form {
  my %args = @_;
  my $SUB_NAME = "create_request_form";

  #### Process the arguments list
  my $ref_parameters = $args{'ref_parameters'}
    || die "ref_parameters not passed";
  my %parameters = %{$ref_parameters};
  my ($sql, @rows);
  my $html;
  my $o_conc=0.00025; #hard-coded default Oligo concentration
  my $s_conc=50; #hard-coded default salt concentration

  #--------------- print_form_head ---------------#
  $html = qq~








  
  
  ~;
  print $html;

  #------------ print_search_bs_sets -------------#
  $html = qq~
  
 BioSequence Files:

  

  

    
    Featurama Library:  (used in Featurama search)
    
    
    
    
  

    

    BLAST Library:  (used in BLAST search)
    
    
    
    
  

  

   
   

   Sanity Check:
   

   Are the sequences for which you want features the same as the BLAST Library you\'ve select? 
    
    		
  

  

  ~;
  
  print $html;

  #----------- print_search_parameters -----------#

  $html = qq~
  

  
Search Parameters:

  

  

    
    Oligo Concentration (mMol):
    
    
    
    
    
     Salt Conc. (mMol):
    
    
    
    
  

  

    
    Tm (0-100):
    
    
    +/- (0-50):
    
    
     Step Size (0-100,000):
    
    
    
    
  

  

    
    Min. Reporter Length (2-100):
    
    
    
    
    
     Max. Reporter Length (Min. Length-100):
    
    
    
    
  

  

    
    Max. 3\' Distance (2-150,000):
    
    
    
    
    
     Max. Reporters per Gene (1-10000):
    
     
  

  

    
    Initial 3\' Offset (0-100,000):
    
    
    
    
    
    Max. Self-Comp Score (0-Min. Length):
    
    
    
    
  

  

      ~;
  print $html;

  #----------- print_searh_heuristics -----------#
  $html = qq~
  

  

  
Content Heuristics:

  

  

    
    Max. Poly A/T Length (2-Max. Length):
    
    
    
    
    
    Max. Poly G/C Length (2-Max. Length):
    
    
    
    
  

  

    
    Heuristic Window Size (2-Min. Length):
    
    
    
    
  

  

    
    Max. A/T in Window (1-WindowSize):
    
    
    
    
    
    Max. G/C in Window (1-WindowSize):
    
    
    
    
  

  

  ~;
  print $html;

  #------------ print_search_comments -----------#
  $html = qq~
  

  

  
Comments:

  
  

  

  

  ~;
  print $html;

  #-------------- print_form_foot ---------------#
  $html = qq~
  
  
  
  		






  ~;

  print $html;
  return;

} # end create_request_form



###############################################################################
# verify_parameters
###############################################################################
sub verify_parameters {
  my %args = @_;
  my $SUB_NAME = "verify_parameters";

  #### Process teh arguments list
  my $ref_parameters = $args{'ref_parameters'}
  || die "ERROR[$SUB_NAME]:ref_parameters not passed!\n";
  my %parameters = %{$ref_parameters};
  my $ok = 1;
  my $same_as_lib = $parameters{'same_as_lib'};
  
  # Featurama Lib and BLAST Lib are the same AND not suppose to be
  if (($parameters{'featuramalib'} eq $parameters{'blastlib'}) &&
      ($parameters{'same_as_lib'} eq "No")){
    print "ERROR: Library files are the same.
\n";
    $ok=0;
  }

  # Featurama Lib and BLAST Lib are not the same and supposed to be
  if (($parameters{'featuramalib'} ne $parameters{'blastlib'}) &&
      ($parameters{'same_as_lib'} eq "Yes")) {
    print "ERROR: Library files are not the same.
\n";
    $ok=0;
  }

  # Tm
  my $tm = $parameters{'meltTemp'};
  if ($tm > 100 || $tm < 0 || 
      (length($tm)==0 && !($tm=~/^[+-]?0*[.?0|0.?]0*[[eE]+[+-]?\d*[.?\d|\d.?]\d*]*/))) {
    print "ERROR: Tm is not valid
\n";
    $parameters{'meltTemp'} = "";
    $ok=0;
  }

  # Tm range
  my $tm_range = $parameters{'meltTempRange'};
  if ($tm_range > 50 || $tm_range < 0 ||
      ($tm_range==0 && !($tm =~/^[+-]?0*[.?0|0.?]0*[[eE]+[+-]?\d*[.?\d|\d.?]\d*]*/))) {
    print "ERROR: Tm range is not valid
\n";
    $parameters{'meltTempRange'} = "";
    $ok=0;
  }

  # Oligo Concentration
  if ($parameters{'oligoConc'} <= 0) {
    print "ERROR: Oligo. Conc. is not valid
\n";
    $parameters{'oligoConc'} = "";
    $ok=0;
  }

  # Salt Concentration
  if ($parameters{'saltConc'} <= 0) {
    print "ERROR: Salt Conc. is not valid
\n";
    $parameters{'saltConc'} = "";
    $ok=0;
  }

  # Minimum Length
  my $min_len = $parameters{'minLen'};
  if ($min_len > 100 || $min_len < 1 || !($min_len =~ /^[+-]?\d+$/)) {
    print "ERROR: Min Length is not valid
\n";
    $parameters{'minLen'} = "";
    $ok=0;
  }

  # Maximum Length
  my $max_len = $parameters{'maxLen'};
  if ($max_len > 100 || $max_len < $min_len || 
      $max_len == 0 || !($max_len =~ /^[+-]?\d+$/)) {
    print "ERROR: Max Length is not valid
";
    $parameters{'maxLen'} = "";
    $ok=0;
  }

  # Self Complementarity
  my $self_comp = $parameters{'maxSelfComp'};
  if ($self_comp>$min_len || $self_comp < 0 || !($max_len =~ /^[+-]?\d+$/)) {
    print "ERROR: Max Self-Comp is not valid
\n";
    $parameters{'maxSelfComp'}="";
    $ok=0;
  }

  # Step Size
  my $step = $parameters{'stepSize'};
  if ($step > 100000 || $step < 0 || !($step =~ /^[+-]?\d+$/)) {
    print "ERROR: Step size is not valid
\n";
    $parameters{'stepSize'}="";
    $ok=0;
  }

  # Max 3' Distance
  my $dist = $parameters{'max3PrimeDist'};
  if ($dist > 150000 || $dist < 2 || !($dist =~ /^[+-]?\d+$/)) {
    print "ERROR: Max 3' distance is not valid
\n";
    $parameters{'max3PrimeDist'} = "";
    $ok=0;
  }

  # Initial 3' Offest
  my $offset = $parameters{'initOffset'};
  if ($offset > 100000 || $offset < 0 || !($offset =~ /^[+-]?\d+$/)) {
    print "ERROR: Initial 3' offest is not valid
\n";
    $parameters{'initOffest'} = "";
    $ok=0;
  }
  
  # Maximum Features
  my $features = $parameters{'maxReporters'};
  if ($features > 10000 || $features < 1 || !($features =~ /^[+-]?\d+$/)) {
    print "ERROR: Maximum features is not valid
\n";
    $parameters{'maxReporters'} = "";
    $ok=0;
  }

  # Maximum Poly AT
  my $p_AT = $parameters{'maxPolyAT'};
  if ($p_AT > $max_len || $p_AT < 2 || !($p_AT =~ /^[+-]?\d+$/)) {
    print "ERROR:Maximum Poly-AT is not valid
\n";
    $parameters{'maxPolyAt'} = "";
    $ok=0;
  }

  # Maximum Poly GC
  my $p_GC = $parameters{'maxPolyGC'};
  if ($p_GC > $max_len || $p_GC < 2 || !($p_GC =~ /^[+-]?\d+$/)) {
    print "ERROR:Maximu Poly-GC is not valid
\n"  ;
    $parameters{'maxPolyGC'} = "";
    $ok=0;
  }

  # Window Size
  my $win = $parameters{'windowSize'};
  if ($win > $min_len || $win < 2 || !($win =~ /^[+-]?\d+$/)) {
    print "ERROR: Window size is not valid
";
    $parameters{'windowSize'}="";
    $ok=0;
  }

  # Max AT in Window
  my $win_at = $parameters{'maxATinWindow'};
  if ($win_at > $win || $win_at < 1 || !($win_at =~ /^[+-]?\d+$/)) {
    print "ERROR: Max AT content in window is not valid
";
    $parameters{'maxATinWindow'}="";
    $ok=0;
  }

  # Max GC in Window
  my $win_gc = $parameters{'maxGCinWindow'};
  if ($win_gc > $win || $win_gc < 1 || !($win_gc =~ /^[+-]?\d+$/)) {
    print "ERROR: Max GC content in window is not valid
";
    $parameters{'maxGCinWindow'}="";
    $ok=0;
  }

  # Comments
  my $comments = $parameters{'comments'};
  if ($comments) {
    $comments =~ s/<(.*?)/$1/g;
  }

  return $ok, \%parameters;
}