[Bioperl-l] seqIO and file handle

[Jason Stajich]

This is an autoflush problem, it is fixed in the live code but probably
not in the code you are dealing with.  You just need to close the
Bio::SeqIO object .. $seqio->close() or better $seqio = undef.

BTW, a better way to do what you want below would be to use IO::String to
create a filehandle and just write it rather than the
tempfile and read it back in route. You get your sequence string back out
from the IO::String object.

-jason
On Thu, 25 Jul 2002, Damien Mattei wrote:

>
> i have a problem writing sequence in a temp file with seqIO
> and reading it immediately the end of file is truncated even if it is
> not on disk.
>
> here is my code:
>
> # create temporary sequence file in specific format
> # (genbank, fasta or embl) and write it in text widget
> # param 1 : format (Fasta,GenBank,EMBL)
> # param 2 : sequence
> sub  seqtmptxt {
>
>      my ($format,$seq) = @_;
>      my ($fh, $name_file) = tempfile( SUFFIX => '.' . $format);
>      print $name_file . "\n" ;
>      my $seqio = Bio::SeqIO->new('-format' => $format,-file =>
> ">$name_file");
>      $seqio->write_seq($seq);
>      close($fh);
>      print "Sequence written in tmp file\n";
>      #$scrolled_texte->configure(-state => 'normal');
>      #$scrolled_texte->delete("1.0","end");
>
>      #`tail $name_file`;
>
>      open(TMPFILE,"< $name_file") or goto NOOPEN;
>      my $buffer;
>      while (my $byteread = read(TMPFILE, $buffer, 16384)) {
>      #while (my $record = <TMPFILE> ) {
> 	#print "byte read = $byteread\n";
> 	#$scrolled_texte->insert('end', $buffer);
> 	print $buffer;
>
>      }
>      print $buffer;
>      close TMPFILE or print "impossible to close $name_file : $!";
>      #$scrolled_texte->configure(-state => 'disabled');
>      unlink $name_file;
>      return;
>    NOOPEN:
>      print "impossible to open $name_file : $!";
> }
>
> i comment out all the Tk relative code to don't annoy readers and assume
> the problem is that the problem is with file handler.
> If i add `tail $name_file`; (see in code where it is commented) the file
> display well, so there should be a way to flush this file but i don't
> know how.
>
> Damien
>
> --------------------------------------
> Damien Mattei
> C.N.R.S / U.N.S.A - UMR 6549
> mailto:mattei@unice.fr
> http://www-iag.unice.fr/
> --------------------------------------
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu