[Bioperl-l] Bio::FeatureIO::gff bug?

Chris Fields cjfields at uiuc.edu
Mon Sep 24 09:09:46 EDT 2007


It looks like the first is a cut-and-paste revision of the second, so  
I would say the second independent if block is redundant.

Should we be printing output in _initialize()?  I would think any  
output would be handled in a write_* method of some sort and not in a  
common method used for initializing both input and output stream  
data.  What happens here if you use '-fh' and want output redirected  
to STDOUT?

chris

On Sep 24, 2007, at 4:35 AM, Sendu Bala wrote:

> Hi,
>
> I'm finding that when writing GFF files the version header line gets
> printed out twice. This is because:
>
> sub _initialize {
>    # [snip]
>
>    if ($arg{-file} =~ /^>.*/ ) {
>      $self->_print("##gff-version " . $self->version() . "\n");
>    }
>    else {
>      my $directive;
>      while(($directive = $self->_readline()) && ( $directive =~ / 
> ^##/ ||
> $directive =~ /^>/)){
>        $self->_handle_directive($directive);
>      }
>      $self->_pushback($directive);
>    }
>
>    if ($arg{-file} =~ /^>.*/ ) {
>      $self->_print("##gff-version " . $self->version() . "\n");
>    }
>
>    # [snip]
> }
>
> Does it make sense for if ($arg{-file} =~ /^>.*/ ) to appear twice  
> like
> that? If not, which one should be removed? The independent one, or the
> if/else one?
>
>
> Cheers,
> Sendu.



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