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

Chris Fields cjfields at uiuc.edu
Fri Jun 15 10:05:07 EDT 2007


On Jun 15, 2007, at 2:28 AM, Martin MOKREJŠ wrote:

> 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. ;)

<bring foot to mouth and insert>

Sorry about that.  I notice that '.' was added, but the spacing  
seemed off.  I think bioperl catches that fine but it's something  
Wayne should consider.

>> 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

Horribly named script (should be seq2picture, since it converts both  
gb/embl).  The use of 'all_tags' makes me think the script version  
you are using is old, as those methods have long since been renamed.   
Dave has it working though, so maybe your version has been updated?   
The 'use of initialized data in' errors are probably from inclusion  
of mandatory fields with no data or '.'.

>> 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.

As I said, unless someone shows interest and codes it just won't get  
done.  We have had very little interest in this, either b/c there are  
tools already out there to do this very thing (multitudes of plasmid  
drawing programs, some free like ApE) or that nobody's bothered to  
write it up.

chris




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