[Bioperl-l] append schema to proxy

Roy Chaudhuri roy.chaudhuri at gmail.com
Wed Aug 24 14:21:12 EDT 2011


Hi Galeb,

This is the wrong mailing list for your question - it's intended for 
discussion of the Bioperl toolkit, not general bioinformatics questions. 
Next time, try a general bioinformatics mailing list such as BBB:
http://www.bioinformatics.org/lists/bbb

Having said all that, maybe you could try BRIG:
http://sourceforge.net/projects/brig/
http://www.biomedcentral.com/1471-2164/12/402

Cheers,
Roy.

On 24/08/2011 19:09, galeb abu-ali wrote:
> Hi,
>
> I'm trying to run a program that generates a circular genome homology atlas
> "BLASTatlas" ( http://www.cbs.dtu.dk/ws/ws.php?entry=BLASTatlas ). I think
> the problem is with the module that appends schemas to the proxy, and I
> don't know how to do that manually. I've emailed the author couple times and
> have not heard back. Pasted below is the error message. At your convenience,
> I'd greatly appreciate your help.
>
> thanks
>
> galeb
>
> p/s - also, is there another program that can generate concetric circular
> plots of BLAST scores for multiple bacterial genomes with a per nucleotide
> resolution? thanks
>
> [galeb at localhost GeneWiz]$ BLASTatlas -modus circle -ref BX571966.fsa
> -proteins BX571966.proteins.fsa -ann BX571966.ann -blastcfg blast.cfg
> -customcfg custom.cfg --dnap="Intrinsic Curvature,Stacking Energy,Position
> Preference" -title "B. pseudomallei K96243">   sgeneric.ps
> # title set to 'B. pseudomallei K96243'
> # output format is ps
> # modus is 'circle'
> # loading reference genome ...
> # loading proteins ...
> # parsing blast lane configuration (blast.cfg) ...
> # .. parsing blast lane (B. ubonensis Bu) ...
> # .. .. program: tblastn
> # .. .. parsing color 101010_040410
> # .. .. .. color from: r:10, g:10, b:10
> # .. .. .. color to: r:04, g:04, b:10
> # .. .. byrange: 0 .. 0.8
> # .. parsing sequene source 'cat ./19539.fsa |' ... 1142 done
> # .. parsing blast lane (B. pseudomallei DM98) ...
> # .. .. program: tblastn
> # .. .. parsing color 101010_040410
> # .. .. .. color from: r:10, g:10, b:10
> # .. .. .. color to: r:04, g:04, b:10
> # .. .. byrange: 0 .. 0.8
> # .. parsing sequene source 'cat ./19509.fsa |' ... 2370 done
> # parsing custom lane configuration (custom.cfg) ...
> # .. parsing custom data entry SIDD at -0.035 ...
> # .. .. parsing color 000010_101010
> # .. .. .. color from: r:00, g:00, b:10
> # .. .. .. color to: r:10, g:10, b:10
> # .. .. byrange: 9 .. 10
> # .. .. boxfilter 5000 ...
> # .. parsing data source 'gunzip -c
> BX571966-57a2f2c2e11ca0dd8cd74493d667d4d6-3173005.sidd--0.035-c-10-c.out.gz
> | cut -f4 |' ...
> # .. .. parsing data source ... 3173005 done
> # reading external files and build hash of sequences ...
> *panic: schemas() removed in v2.00, not needed anymore*
>   at /usr/local/lib/perl5/site_perl/5.12.2/XML/Compile/WSDL11.pm line 65
> XML::Compile::WSDL11::schemas(XML::Compile::WSDL11=HASH(0x1fed6740)) at
> xml-compile.pl line 48
> main::appendSchemas(XML::Compile::WSDL11=HASH(0x1fed6740), "
> http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd", "
> http://www.cbs.dtu.dk/ws/BLASTatlas/ws_blastatlas_1_0_ws2.xsd") at
> BLASTatlas line 177
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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