[Bioperl-l] Re: newbie needs help with read/write Genbank

[Hilmar Lapp]

Since you are not posting an exception I'm assuming there is none; 
instead you observe that bioperl does not 100% round-trip.

This is a known problem that hasn't received priority high enough so 
that somebody would volunteer to address it. What we've focused on in 
this context is to make sure that Bioperl can read files that it writes 
without barfing, not that the result will match the origin 100%. You 
are welcome to address this if it is important to you.

	-hilmar

On Monday, April 4, 2005, at 09:29  PM, Jonathan Miller wrote:

>
> One might have hoped this code would read and write
> a Genbank file, unchanged. But no. how then?
> -------------------------------------------------------
>
> use Bio::SeqIO;
>
> my $infile=shift;
> $in  = Bio::SeqIO->new(-file => $infile,
>                        -format => 'GenBank'
>                         );
> my $outfile= ">" . $infile . ".gbk";
> $out = Bio::SeqIO->new(-file => $outfile,
>                        -format => 'GenBank'
>                         );
>
> while ( $seq = $in->next_seq() ) {
>  $out->write_seq($seq);
> }
>
>
>
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>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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