[Bioperl-l] <No subject>

[Jason Stajich]

On Wed, 29 May 2002 AUnderwood@PHLS.org.uk wrote:

> I would be very greatful for anybody's  help with this bioperl problem:
> I am using seqIO with the "newFh coomand) e.g
> $in = Bio::SeqIO->newFh(-file => "inputfilename" , '-format' => 'Fasta');
> $out = Bio::SeqIO->newFh(-file => "outputfilename" '-format' => 'Genbank');
> print $out $_ while <$in>;
> However although this writes the outputfilename file correctly, if I try to
> read this file in in the next line e.g
> open(TEMP, "C:/TB/temp.gbk") || die "Cannot open file
> \"/tmp/Sequences/TB/temp.gbk\" \n";
> @temp =<TEMP>;
> close TEMP;
> print @temp;
>
> Only part of the file is read (misses the last 50 lines). If I read the file
> with the same lines but in a standalone script it works fine.
>
$out->close();
and/or
undef $out;

> Please can you tell me how to close the filehandle specified in the $out
> line.
> Any help on how this can be achieved/problem solved would be much
> appreciated,
>
>
> Dr Anthony Underwood
> Bioinformatics Unit
> Central Public Health Laboratory
> 61 Colindale Avenue
> London
> NW9 5HT
> t:    0208 2004400 ext. 3618
> f:    0208 3583138
> e: aunderwood@phls.org.uk
>
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu