[Bioperl-l] How to draw a plasmid map from a genbank-formatted file?

Dave Howorth dhoworth at mrc-lmb.cam.ac.uk
Fri Jun 15 04:59:09 EDT 2007


Martin MOKREJŠ wrote:
>>> Also, there is a *huge* amount of documentation and examples on
>>> the BioPerl website.
>>> 
>>> http://www.bioperl.org/wiki/HOWTOs
>> You mean 
>> http://www.bioperl.org/wiki/HOWTO:Graphics#Rendering_Features_from_a_GenBank_or_EMBL_File
>>  ? ;-)
> 
> $ perl embl2picture.pl ~/99.gb | display - Error returned while
> evaluating value of 'description' option for glyph
> Bio::Graphics::Glyph::generic=HASH(0x8aa5790), feature
> Bio::Location::Simple=HASH(0x893ebc4): Can't locate object method
> "all_tags" via package "Bio::Location::Simple" at embl2picture.pl
> line 141, <GEN0> line 125.

Hmm an error at line 141 of a 69 line script? Methinks you're not
actually running the script that's presented on the wiki page you
quoted. I cut-and-pasted the script and your file and it worked for me
(at least, it produced an image, along with a bunch of OOPS lines)

HTH, Dave


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