[Bioperl-l] bsml -XML

Brian Osborne brian_osborne at cognia.com
Fri May 28 07:26:26 EDT 2004


According to the INSTALL file you need to install XML::DOM in order to use
SeqIO with the BSML format.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of hafiz hafiz
Sent: Friday, May 28, 2004 2:31 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] bsml -XML

please some one can help me,i have transfer my
database used seqIO ,i can transfer most of type
database but not bsml- xml

this my code;

#! usr\bin\perl

use Bio::Root::IO;
use Bio::SeqIO;
use Bio::Seq;
use Bio::Seq::RichSeq;
use Location;

$format = swiss;

#Load  module Location.pm into an array
@filelocation = Location::filelocation ("sprot42.dat",

#Access directory path that resides in second element
of array @filelocation
 my $location = $filelocation[1];

chdir $location;
# chdir $location1;
        print " location directory database

#Open the directory that are returned by Location.pm
 opendir (DIR, $location)|| die "\nCouldn't open
directory or directory not found\n";

#Read the drectory and store its content in an array
  @file = readdir (DIR);

foreach $file(@file) {

  if ($file eq "sprot42.dat") {


print "\nEnter filename for output file:";
chomp ($outFile = <STDIN>);

print "\nEnter format for output file:";
chomp ($format1 = <STDIN>);

print"\n........Chance funtion.......\n";

#chance format function

my $seq_in = Bio::SeqIO->new(-file=>$file,'-format'=>

my $seq_out =

  my $inseq;
          while ( $inseq = $seq_in->next_seq) {

        #Method from Bioperl module-Bio::SeqIO
        #Create a sequence object and store it in
scalar variable
        $in = Bio::SeqIO->new(-file

    }#End first if loop

}#End foreach loop

this is my output while i transfer to bsml ;

Undefined subroutine &XML::DOM::DocumentType called at
/usr/lib/perl5/vendor_perl/5.8.0/XML/DOM.pm line 3475,
<GEN0> line 53.

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