[Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Jun 5 14:56:58 EDT 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2305





------- Comment #3 from mmokrejs at ribosome.natur.cuni.cz  2007-06-05 14:56 EST -------
Wayne Davis wrote:
> locus line I'm using is the old standard (some older parsers wanted it 
> that way).
> I've updated to write the new standard, if your program isn't flexible 
> enough to read the old style locus lines. We'll see if anyone is using 
> the older parsers still.
> from the document laying out the new standard:
> 
>  We encourage software developers to switch to a token-based LOCUS parsing
> approach, rather than a column-specific approach. If this is done, then future
> changes to the LOCUS line that affect only the spacing of its data values will
> 
> not require any modifications to software.
> 
> 
> 
> 
> I've made the default behavior to put "." in the empty fields. I left 
> those fields there because there are other parsers that require them.
> In my new version you can change the default genbank record values by 
> adding a line to your preferences file like this:
> empty_genbank_header<TAB>{LOCUS       } {} {DEFINITION  } {.} 
> {ACCESSION   } {.} {VERSION     } {.} {SOURCE      } {.} {  ORGANISM  } {.}
> 
> or
> empty_genbank_header<TAB>{LOCUS       } {}
> 
> 
> My access to our web server is temporarily unavailable, but I'll post 
> the update as soon as I can.


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