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

Martin MOKREJŠ mmokrejs at ribosome.natur.cuni.cz
Thu Jun 14 13:23:28 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.

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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