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

[Martin MOKREJŠ]

Hi Chris,

Chris Fields wrote:
> 
> 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.

Would you please tell me exactly what is wrong with the spacing?

> 
>>> 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 '.'.

Well, I just copy&pasted the script from the bioperl webpages, I think
from a tutorial or FAQ, don't remember anymore.

> 
>>> 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.

Well, my search for such tools available on Unix to be used in a script,
non-interactively, completely failed. My last hope except getting improved
ApE is to use the GenomeDiagram under biopython, but so far my .gb files
cannot be parsed yet. :(
Martin