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undefined value error

Posted on 2004-10-02
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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
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Question by:jingks03
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4 Comments
 
LVL 84

Expert Comment

by:ozo
ID: 12210452
What is fastream?
0
 

Accepted Solution

by:
stefzodiak earned 1000 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

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