[Bioperl-l] Bug in the Bio::SeqIO.scf.pm code

Chris Fields cjfields at uiuc.edu
Mon Jan 29 08:21:51 EST 2007


Could you add a test file for the bug to the bug report or send it to  
me?  If you send it make sure not to CC the entire mail list.

I'll commit this to CVS once we have a test in place.

chris

On Jan 29, 2007, at 5:29 AM, Anthony Underwood wrote:

> Hi All,
>
>
>
> Has anybody else come across this problem:
>
>
>
> I have some scf files that fail to be read by the next_seq method  
> within
> scf.pm due to line 226: my $name_comment = $name_comments[0]- 
> >as_text();
>
> Error: can not call method as_text on undefined object.
>
>
>
> It appears that if the scf file has no comments then the array
> @name_comments created in the previous line is empty.
>
>
>
> I overcame this by replacing line 226 with the following lines:
>
> my $name_comment;
>
> if (@name_comments){
>
>      $name_comment = $name_comments[0]->as_text();
>
>      $name_comment =~ s/^Comment:\s+//;
>
> }
>
>
>
>
>
> Should this be incorporated into the code? Many thanks,
>
>
>
> Anthony
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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