[Bioperl-l] XML::DOM and bsml-Xml?
hafiz hafiz
khufaz83 at yahoo.com
Tue Jun 8 04:02:41 EDT 2004
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",
$database);
#Access directory path that resides in second element
of array @filelocation
my $location = $filelocation[1];
chdir $location;
# chdir $location1;
print " location directory database
swissprot:$location\n";
#Open the directory that are returned by Location.pm
modul
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"\n CHANCE FORMAT FUNCTION\n";
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'=>
"$format");
my $seq_out =
Bio::SeqIO->new(-file=>">$outFile",'-format'=>
"$format1");
my $inseq;
while ( $inseq = $seq_in->next_seq) {
$seq_out->write_seq($inseq);
}
#Method from Bioperl module-Bio::SeqIO
#Create a sequence object and store it in
scalar variable
$in = Bio::SeqIO->new(-file
=>$file,'-format'=>"$format");
}#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.
thank you to Brian Osborne i have install XML::DOM and
XML::Parser but i still can't tarsfer to bsml and get
a same output.
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