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

Chris Fields cjfields at uiuc.edu
Thu Jun 14 13:46:38 EDT 2007


Is 99.gb supposed to be a GenBank file?  And you're loading it into  
embl2picture (which I assume takes EMBL format files)?  Without  
example code we can easily make the wrong assumptions (i.e. that this  
is user error and not a BioPerl problem).

Also, I don't believe the feature plotting scripts plot circular  
chromosomes/plasmids.  If you want this functionality you'll have to  
code it for yourself.

chris

On Jun 14, 2007, at 12:23 PM, Martin MOKREJŠ 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.
>
> Error returned while evaluating value of 'description' option for  
> glyph Bio::Graphics::Glyph::generic=HASH(0x8aa57f0), feature  
> Bio::Location::Simple=HASH(0x893ebb8): Can't locate object method  
> "all_tags" via package "Bio::Location::Simple" at embl2picture.pl  
> line 141, <GEN0> line 125.
>
> Error returned while evaluating value of 'description' option for  
> glyph Bio::Graphics::Glyph::generic=HASH(0x8aa5880), feature  
> Bio::Location::Simple=HASH(0x893ebac): Can't locate object method  
> "all_tags" via package "Bio::Location::Simple" at embl2picture.pl  
> line 141, <GEN0> line 125.
>
> Error returned while evaluating value of 'description' option for  
> glyph Bio::Graphics::Glyph::generic=HASH(0x8aa5430), feature  
> Bio::Location::Simple=HASH(0x893e720): Can't locate object method  
> "all_tags" via package "Bio::Location::Simple" at embl2picture.pl  
> line 141, <GEN0> line 125.
>
> Error returned while evaluating value of 'description' option for  
> glyph Bio::Graphics::Glyph::generic=HASH(0x8aa546c), feature  
> Bio::Location::Simple=HASH(0x893e6b4): Can't locate object method  
> "all_tags" via package "Bio::Location::Simple" at embl2picture.pl  
> line 141, <GEN0> line 125.
> $
>
> The plasmid is a circular DNA, why is the diagram in linear? ;-)
>
> Martin
>
>
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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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