Solved

undefined value error

Posted on 2004-10-02
4
276 Views
Last Modified: 2008-03-17
my test.cgi can be excuted at command mode with "perl test.cgi", however it has some error called "sequence method cannot be called for undefined value error" happened at one line (indicated by ***** in the code )calling one method of another module. Before that line, everything is ok.

The code for test.cgi is following (followed by the code of module DNAalign.pm):

Can anybody help me figure out the problem?

thanks,

#!/usr/bin/perl

use strict;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
use warnings;
use diagnostics;
use File::Basename;
use DNAalign;
use fastream;
use DNAseq;

my $query = new CGI;
my ($defaultfolder,$project)=split(/&/,$ENV{'QUERY_STRING'});
print "Content-type: text/html\n\n";

print "<html><head><title>Perl CGI Example # 2";
print "</title></head><body><h1>";
print "Alignment Result </h1><p>";
print "<pre>";


my $strk="/srv/www/httmp/$defaultfolder/$project/chromat_dir";
chdir($strk);
my $upload_filehandle = $query->upload("alignFile");
open UPLOADFILE, ">/srv/www/httmp/$defaultfolder/$project/chromat_dir/secondFile";
while ( <$upload_filehandle> )
{
   print UPLOADFILE;
}
close UPLOADFILE;
my $pfile1="$project.fasta.screen.contigs.qual";
open(INPUT2, "<","$project.fasta.screen.contigs.qual" )
or die "Could not open the file for reading: $!\n";
my @logData2 = <INPUT2>;
close(INPUT2);

my $size=@logData2;

my @arr3=();
for(my $i=1;$i<$size;$i++){
  chomp $logData2[$i];
  my @brr3=split(/ /,$logData2[$i]);
  push(@arr3,@brr3);
}
my $pfile="secondFile";
my $str="/srv/www/httmp/$defaultfolder/$project/chromat_dir";
chdir($str);
my $seq1=fastream->new("$project.fasta.screen.contigs");
my $seq2=fastream->new("secondFile");

my $test1=$seq1->next_seq();
print "$test1";
my $test2=$seq2->next_seq();
print "$test2";

my ($result1,$result2);
($result1,$result2) = DNAalign::align($test1,$test2);

*****my $str1=$result1->sequence();
my $str2=$result2->sequence();

my @arrStr1=split(//,$str1);
my @arrStr2=split(//,$str2);
my $siz=@arrStr1;
my $count=0;
for(my $c1=0;$c1<(int $siz/30)+1;$c1++){
  my $start=$c1*30+1;
  my $stop=$c1*30+30;
  my $str="$start"."-"."$stop"." ";
  print "$str";
  my $l=11-(length $str);
  for(my $len=0;$len<$l;$len++){
     print " ";
  }

 for(my $c2=0;$c2<30;$c2++){
    if($arrStr1[30*$c1+$c2] eq $arrStr2[30*$c1+$c2]){
      print "<font color=\"green\">$arrStr1[30*$c1+$c2]</font>";
          print "  ";
    }else{
      print "<font color=\"red\">$arrStr1[30*$c1+$c2]</font>";
          print "  ";
    }
  }      
  print "\n";
  my $str3="alignment  ";
  print "<font color=\"orange\">$str3</font>";
  for(my $c2=0;$c2<30;$c2++){
    if($arrStr1[30*$c1+$c2] eq $arrStr2[30*$c1+$c2]){
      print "<font color=\"green\">$arrStr2[30*$c1+$c2]</font>";
          print "  ";
    }else{
      print "<font color=\"red\">$arrStr2[30*$c1+$c2]</font>";
          print "  ";
    }
  }
  print "\n";
 
  my $str4="confidence ";
  print "<font color=\"orange\">$str4</font>";
  for(my $c2=0;$c2<30;$c2++){
    if($arrStr1[30*$c1+$c2] ne "-"){
      print "<font color=\"blue\">$arr3[$count]</font>";
        print " ";
        if((int $arr3[$count])<10){print " ";}
        $count++;
    }else{
      print "   ";
    }
  }
  print "\n";  
  print "\n";
}


print "</pre>";
print "</p>";

print "</body></html>";


____________________
code for DNAalign.pm


# Keith Anthony Boroevich -- 24.11.2003

package DNAalign;
use strict;
use Carp;
use diagnostics;
use File::Temp 'tempfile', 'tempdir';
use fastream;

my $tdir = tempdir('DNAalignXXXXX', TMPDIR => 1, CLEANUP => 1);

BEGIN { }

sub align {
    my $seq1 = shift;
    my $seq2 = shift;
    my %options = (
               ALGORITHM => 'lagan',
               FILENAME => undef,
               STYLE => undef,
               );
    %options = (%options, @_) if @_;

    # --- align sequences --- #
    my @aseq;
    if    (uc($options{ALGORITHM}) eq 'LAGAN')   { @aseq = lagan($seq1,$seq2); }
    elsif (uc($options{ALGORITHM}) eq 'CLUSTAL') { croak "Clustal not yet supported.\n"; return ($seq1,$seq2); }
    # elsif other formats
    else { croak "Unknown Algorithm: ",$options{ALGORITHM},".\n"; return ($seq1,$seq2); }

    #--- output file if requested ---#
    if (defined($options{FILENAME})) {
      open OFILE, ">$options{FILENAME}";
      if ((uc($options{STYLE}) eq 'FASTA')||(! $options{STYLE})) {
          foreach my $aseq (@aseq) { print OFILE "$aseq"; }
      } elsif (uc($options{STYLE}) eq 'CLUSTAL') {
          print OFILE clustal_format(@aseq);
      }
      close OFILE;
    }
    return (@aseq);
}


sub lagan {
    my $seq1 = shift;
    my $seq2 = shift;

    # --- create sequence files --- #
    my ($ofh1,$ofile1) = tempfile( TEMPLATE => 'kabXXXXX', SUFFIX => '.fas', UNLINK => 1, DIR => $tdir);
    print $ofh1 "$seq1";
    system("/data/software/RepeatMasker/current/RepeatMasker -qq -int -nocut $ofile1 > /dev/null");
    my ($ofh2,$ofile2) = tempfile( TEMPLATE => 'kabXXXXX', SUFFIX => '.fas', UNLINK => 1, DIR => $tdir);
    print $ofh2 "$seq2";
    system("/data/software/RepeatMasker/current/RepeatMasker -qq -int -nocut $ofile2 > /dev/null");

    # --- align sequences --- #
    my ($ifh, $ifile) = tempfile( TEMPLATE => 'kabXXXXX', SUFFIX => '.fas', UNLINK => 1, DIR => $tdir);
    close($ifh);
    #print `/data/software/lagan/current/lagan.pl $ofile1 $ofile2 -mfa > $ifile`; # With lagan reporting
    system("/data/software/lagan/current/lagan.pl $ofile1 $ofile2 -mfa > $ifile 2> /dev/null");
    my $istream = fastream->new($ifile);
    my @seqs;
    while (my $seq = $istream->next_seq()) { push @seqs, $seq; }
    return @seqs;

}

sub clustal_format {
    my @seqs = @_;
    my $count = $#seqs;
    my $minlength = $seqs[0]->length();
    foreach (@seqs) {
      $minlength = $_->length() if $_->length() < $minlength;
    }
    my $cf = "CLUSTAL X (1.8) multiple sequence alignment\n\n";
    for (my $i = 0; $i < $minlength; $i+=50) {
      foreach (@seqs) {
          $cf .= $_->id().' '.$_->subseq($i,50)."\n";
      }
      $cf .= "\n";
    }
    return $cf;
}

END { }

1;

0
Comment
Question by:jingks03
4 Comments
 
LVL 84

Expert Comment

by:ozo
ID: 12210452
What is fastream?
0
 

Accepted Solution

by:
stefzodiak earned 250 total points
ID: 12213855
Your returning an array from your function DNAlign::align
whereas your trying to put the return values into two scalars.

so, check that the values are defined before passing them
back. On top of that, before you call the object result1 to
invoke the method 'sequence', you should also 'bless' the
variable the appropiate class (which i dont see in the source
you have provided).

hope this helps.
Stef

0

Featured Post

Enabling OSINT in Activity Based Intelligence

Activity based intelligence (ABI) requires access to all available sources of data. Recorded Future allows analysts to observe structured data on the open, deep, and dark web.

Join & Write a Comment

Suggested Solutions

A year or so back I was asked to have a play with MongoDB; within half an hour I had downloaded (http://www.mongodb.org/downloads),  installed and started the daemon, and had a console window open. After an hour or two of playing at the command …
In the distant past (last year) I hacked together a little toy that would allow a couple of Manager types to query, preview, and extract data from a number of MongoDB instances, to their tool of choice: Excel (http://dilbert.com/strips/comic/2007-08…
Explain concepts important to validation of email addresses with regular expressions. Applies to most languages/tools that uses regular expressions. Consider email address RFCs: Look at HTML5 form input element (with type=email) regex pattern: T…
This video shows how to remove a single email address from the Outlook 2010 Auto Suggestion memory. NOTE: For Outlook 2016 and 2013 perform the exact same steps. Open a new email: Click the New email button in Outlook. Start typing the address: …

747 members asked questions and received personalized solutions in the past 7 days.

Join the community of 500,000 technology professionals and ask your questions.

Join & Ask a Question

Need Help in Real-Time?

Connect with top rated Experts

11 Experts available now in Live!

Get 1:1 Help Now