[Bioperl-l] Re: [Gmod-gbrowse] trouble loading "0"

[Lincoln Stein]

Hi Michael,

The fix for this is in the latest bioperl CVS.  I'm afraid you will 
have to wait a while before it is officially released.   Here's a 
patch in case you want to patch the released version.

	13 May 2004 22:55:28 -0000	1.113
--- Bio/DB/GFF.pm	9 Jun 2004 17:13:20 -0000	1.114
***************
*** 1,4 ****
! # $Id: GFF.pm,v 1.113 2004/05/13 22:55:28 avilella Exp $
  
  =head1 NAME
  
--- 1,4 ----
! # $Id: GFF.pm,v 1.114 2004/06/09 17:13:20 lstein Exp $
  
  =head1 NAME
  
***************
*** 3317,3323 ****
    for (@groups) {
  
      my ($tag,$value) = /^(\S+)(?:\s+(.+))?/;
!     $value ||= '';
      if ($value =~ /^\"(.+)\"$/) {  #remove quotes
        $value = $1;
      }
--- 3317,3323 ----
    for (@groups) {
  
      my ($tag,$value) = /^(\S+)(?:\s+(.+))?/;
!     $value = '' unless defined $value;
      if ($value =~ /^\"(.+)\"$/) {  #remove quotes
        $value = $1;
      }
Lincoln

On Wednesday 09 June 2004 11:05 am, Michael Cipriano wrote:
> Why do I have trouble loading the value of zero from
> bp_bulkload_gff.pl
>
> Here is a line from my gff file.
>
> supercontig_718 FUZZNUC Transcription   4597    4603    7.000   -
> .       Sequence "polyA_signal_1" ; Mismatch 0 ;
>
> I have tried doing this also
>
> Mismatch "\0" ;
> And this
> Mismatch "0" ;
>
> All of them just load an empty string into the database
>
> Mismatch "0" and Mismatch 0 both will show as a Note when viewed by
> gbrowse_details (eg Note: Mismatch)
> Mismatch "\0" will show as
> (Mismatch:  ) (empty string)
>
> Any other number or letter shows up just fine, except 0.
>
> Michael Cipriano (mcipriano at mbl.edu)
> Research Assistant I, Global Infectious Diseases
> Josephine Bay Paul Center, Marine Biological Laboratory
> 7 MBL Street, Woods Hole, MA 02543-1015
> Phone: 508-548-3705 (x6707)
> Fax: 508-457-4727
>
>
>
>
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724