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

[Martin MOKREJŠ]

David Messina wrote:
> Hi Martin,
> 
> You're in luck -- the BioPerl core distribution includes two scripts  
> for doing just that:
> 
> 	genbank2gff

Somehow these scripts were not installed for me on Gentoo, but I have then in the
cvs copy. ;-) Anyway, the one above is not for me, I do not need the GFF database,
or better to say I have no intent to install that unknown thing, seems like an overkill
for my case. I just want to render a plasmid map.

> 	genbank2gff3

This one seems more promising but still with current cvs checkout I get...

$ perl /home/mmokrejs/proj/bioperl/bioperl-live/blib/script/bp_genbank2gff3.pl --in stdin --out stdout < ~/99.gb 
# Input: stdin
Use of uninitialized value in split at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 1335, <FH> line 7.
Use of uninitialized value in quotemeta at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 1338, <FH> line 7.
Can't call method "binomial" on an undefined value at /home/mmokrejs/proj/bioperl/bioperl-live/blib/script/bp_genbank2gff3.pl line 675, <FH> line 125.
$
$ bp_seqconvert.pl --from genbank --to embl < ~/IRESite/gb/99.gb 
Use of uninitialized value in split at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 1335, <STDIN> line 7.
Use of uninitialized value in quotemeta at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 1338, <STDIN> line 7.
ID   unknown; SV 1; circular; unassigned DNA; STD; UNC; 5391 BP.
XX
AC   unknown;
XX
XX
XX
CC   ApEinfo:methylated:0
...

Oh dear, I have just manually edited the files and still they are wrong? Oh no. :(

> 
> Look in the scripts directory of the distro.
> 
> 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 ? ;-)

> 
> Reading those, reading the FAQ, and searching the mailing list  
> archives are where I look first when I don't know how to do something  
> in BioPerl.
> 
> 
> Dave
> 
> --
> Dave Messina
> Senior Analyst, Assembly Group
> Genome Sequencing Center
> Washington University
> St. Louis, MO
> 
> 
> 
> 
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> 
> 

-- 
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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