[Bioperl-l] How to draw a plasmid map from a genbank-formatted file?
mmokrejs at ribosome.natur.cuni.cz
Thu Jun 14 13:19:42 EDT 2007
David Messina wrote:
> Hi Martin,
> You're in luck -- the BioPerl core distribution includes two scripts
> for doing just that:
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.
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.
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.
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 Messina
> Senior Analyst, Assembly Group
> Genome Sequencing Center
> Washington University
> St. Louis, MO
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
Dr. Martin Mokrejs
Dept. of Genetics and Microbiology
Faculty of Science, Charles University
Vinicna 5, 128 43 Prague, Czech Republic
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