[Bioperl-l] Query for parseing Genbank files with BioGraphics

[Soumyadeep nandi]

Hi Everybody,

I've installed bioperl-live cvs version in my system.

I've followed the following steps to install
bioperl-live cvs version:
1. cvs -d
:pserver:cvs@cvs.bioperl.org:/home/repository/bioperl
login
2. password "cvs"
3. cvs -z 3 -d
:pserver:cvs@cvs.bioperl.org:/home/repository/bioperl
co -r branch-07 bioperl-live
These i've followed from site
"http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/EasiestEnsemblMirror.html"

But when I run embl2picture.pl which render embl or
genbank file into pictorial form.
I get error that i am pasting below.

Moreover, when I try to parse the blast output file I
get the message
(perhaps you forgot to load
"Bio::Tools::BPlite::HSP"?)
(perhaps you forgot to load "Bio::SearchIO"?)

Please suggest me how do I fix these problems.

With regards,
Soumyadeep

-------------------- EXCEPTION --------------------
MSG: Attempting to set the sequence to
[DEFINITIONEscherichiacoliCFT073section15of18ofthecompletegenome.ACCESSIONAE016769AE014075VERSIONAE016769.1GI:26110701KEYWORDS.SOURCEEscherichiacoliCFT073ORGANISMEscherichiacoliCFT073Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriaceae;Escherichia.REFERENCE1(bases1to301566)AUTHORSWelch,R.A.,Burland,V.,Plunkett,G.D.III,Redford,P.,Roesch,P.,Rasko,D.A.,Buckles,E.L.,Liou,S.-R.,Boutin,A.,Hackett,J.,Stroud,D.,Mayhew,G.F.,Rose,D.J.,Zhou,S.,Schwartz,D.C.,Perna,N.T.,Mobley,H.L.T.,Donnenberg,M.S.andBlattner,F.R.TITLEExtensiveMosiacStructureRevealedbytheCompleteGenomeSequenceofUropathogenicEscherichiacoliJOURNALProc.Natl.Acad.Sci.U.S.A.(2002)InpressREFERENCE2(bases1to301566)AUTHORSWelch,R.A.,Burland,V.,Plunkett,G.D.III,Redford,P.,Roesch,P.,Rasko,D.A.,Buckles,E.L.,Liou,S.-R.,Boutin,A.,Hackett,J.,Stroud,D.,Mayhew,G.F.,Rose,D.J.,Zhou,S.,Schwartz,D.C.,Perna,N.T.,Mobley,H.L.T.,Donnenberg,M.S.andBlattner,F.R.TITLEDirectSubmissionJOURNALSubmitted(20-JUN-2002)GeneticsLaboratory,UniversityofWisconsin-Madison,445HenryMall,Madison,WI53706,USAFEATURESLocation/Qualifierssource1..301566/organism="EscherichiacoliCFT073"/strain="CFT073"/db_xref="taxon:199310"genecomplement(72..1100)/gene="waaW"/note="c4450"CDScomplement(72..1100)/gene="waaW"/note="Residues1to341of342are98.24pctidenticaltoresidues1to341of341fromGenPept.129:]
which does not look healthy
STACK Bio::PrimarySeq::seq
/home/soumya/Download/bioperl/bioperl-live/Bio/PrimarySeq.pm:250
STACK Bio::PrimarySeq::new
/home/soumya/Download/bioperl/bioperl-live/Bio/PrimarySeq.pm:225
STACK Bio::Seq::new
/home/soumya/Download/bioperl/bioperl-live/Bio/Seq.pm:132
STACK Bio::SeqIO::fasta::next_primary_seq
/home/soumya/Download/bioperl/bioperl-live/Bio/SeqIO/fasta.pm:130
STACK Bio::SeqIO::fasta::next_seq
/home/soumya/Download/bioperl/bioperl-live/Bio/SeqIO/fasta.pm:85
STACK toplevel render4.pl:28
-------------------------------------------


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