[BioPython] [Bioperl-l] How to draw a plasmid map from a genbank-formatted file?
Martin MOKREJŠ
mmokrejs at ribosome.natur.cuni.cz
Mon Jun 25 16:05:04 UTC 2007
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
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