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

Martin MOKREJŠ mmokrejs at ribosome.natur.cuni.cz
Mon Jun 25 12:06:24 EDT 2007



Dave Howorth wrote:
> 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)

Maybe you used the first version of the script?  There are two or more
scripts, I used the very last one.

M.




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