[Bioperl-l] Conflicting CGI.pm with Bio::Tools::GuessSeqFormat ?

Lincoln Stein lstein at cshl.edu
Mon Jun 5 10:51:52 EDT 2006


Hi,

From the Synopsis for GuessSeqFormat:

           # To guess the format from an already open filehandle:
           my $guesser = new Bio::Tools::GuessSeqFormat( -fh => $filehandle );
           my $format  = $guesser->guess;
           # If the filehandle is seekable (STDIN isn't), it will be
           # returned to its original position.

The filehandle returned by CGI.pm is not seekable.

Lincoln

On Monday 05 June 2006 04:16, Wijaya Edward wrote:
> Dear Lincoln and experts
>
> Curently I have a CGI application that does this:
>
> 1.  read and uploaded file
> 2. check the content of the file whether fasta or not
> 3. print out the content of the file.
>
>
> Now the problem I'm facing is that
> on step three. The content of the file handled is altered
> namely the very first line does not get printed.
>
> So for example if "test1.fasta" looks like this:
> >Seq0
>
> ATCGGGGG
>
> >Seq1
>
> GGGGGGG
>
> >Seq2
>
> ATCCCCCC
>
> When it was printed it gives only:
>
> ATCGGGGG
>
> >Seq1
>
> GGGGGGG
>
> >Seq2
>
> ATCCCCCC
>
> Why is this happening?
>
> Below is the complete cgi script that
> does the task  I mentioned earlier.
>
> Did I missed out anything in my code?
>
>
>
> __BEGIN__
> #!/usr/bin/perl -w
>
> use CGI qw/:standard :html3/;
> use CGI::Carp qw( fatalsToBrowser );
> use Data::Dumper;
>
> BEGIN {
>     if ( $ENV{PERL5LIB} and $ENV{PERL5LIB} =~ /^(.*)$/ ) {
>
>         # Blindly untaint.  Taintchecking is to protect
>         # from Web data;
>         # the environment is under our control.
>         eval "use lib '$_';" foreach (
>             reverse
>             split( /:/, $1 )
>         );
>     }
> }
>
>
> use Bio::Tools::GuessSeqFormat;
>
> print header,
>     start_html('file upload'),
>     h1('file upload!');
> print_form()    unless param;
> print_results() if param;
> print end_html;
>
> sub print_form {
>     print start_multipart_form(),
>        filefield(-name=>'upload',-size=>60),br,
>        submit(-label=>'Upload File'),
>        end_form;
> }
>
> sub print_results {
>     my $length;
>     my $file = param('upload');
>     my $fh_upload = upload('upload');
>
>     my $guesser_upload = new Bio::Tools::GuessSeqFormat( -fh => $fh_upload
> ); my $format_upload  = $guesser_upload->guess;
>
>     if ( !$file ) {
>         print "No file uploaded.";
>         return;
>     }
>     print h2('File name'),      $file;
>     print h2('Format'), $format_upload;
>     print h2('The content is'),br;
>
>     while (<$fh_upload>) {
>
>      # The very first line of the file is not get printed here
>      # Why?
>
>         print;
>         print br;
>         $length += length($_);
>     }
>     print h2('File length'), $length;
> }
>
>
> __END__
>
> Hope to hear from you again.
>
> Regards,
> Edward WIJAYA
> SINGAPORE
>
>
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-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
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