[Bioperl-l] append schema to proxy

galeb abu-ali abualiga2 at gmail.com
Wed Aug 24 14:09:10 EDT 2011


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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