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

Martin MOKREJŠ mmokrejs at ribosome.natur.cuni.cz
Fri Jun 15 03:28:17 EDT 2007


Chris Fields wrote:
> Is 99.gb supposed to be a GenBank file?  And you're loading it into 

Yes, it was attached to the email. ;)

> 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).

use constant USAGE =><<END;
Usage: $0 <file>
   Render a GenBank/EMBL entry into drawable form.
   Return as a GIF or PNG image on standard output.
 
   File must be in embl, genbank, or another SeqIO-
   recognized format.  Only the first entry will be
   rendered.
 
Example to try:
   embl2picture.pl factor7.embl | display -
 
END

> 
> 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.

That's a pitty it does not, but at least if someone could improve the docs. ;)
Unfortunately I don't have the time to rewrite the code myself now,
I need a working, standalone, already available tool. :(
M.

> 
> 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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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> 
> 

-- 
Dr. Martin Mokrejs
Dept. of Genetics and Microbiology
Faculty of Science, Charles University
Vinicna 5, 128 43 Prague, Czech Republic
http://www.iresite.org
http://www.iresite.org/~mmokrejs




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