pep.xml produced by crux is not well-formed

[andreas quandt]

dear list,

when using crux

crux search-for-matches --parameter-file my.params B08-02057.mzXML /
cluster/scratch/malars/databases/AE004092_sp_9606.idx

i get an invalid pep.xml file

xmllint -noout crux-output/search.target.pep.xml
crux-output/search.target.pep.xml:14405: parser error : ParsePI: PI
xml-stylesheet never end ...

^
crux-output/search.target.pep.xml:14405: parser error : Start tag
expected, '<' not found

^

i tried the same without my.params but get the same error.

does anyone of you know what i could possibly do wrong?

cheers,
andreas

[andreas quandt]

dear list,

apparently there are 2 causes for the xml not being valid:

1) the xml-stylesheet tag has to finish with ?
2) at least the xmlns:xsi has to be set

here a header i generated by hand and which produces a valid xml

<?xml-stylesheet type="text/xsl" href=""?>
<msms_pipeline_analysis date="Wed Feb 2 14:29:47 2011
" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://
www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-
web.systemsbiology.net/pepXML /usr/local/tpp/schema/pepXML_v110.xsd"
summary_xml="">


cheers,
andreas

[B. Frewen]

Hello All,

Many thanks to Andreas for finding this bug and its solution. We will
include the fix in the next release. Please contact me if you have any
further questions.

Thanks,
Barbara

> --
> You received this message because you are subscribed to the Google Groups "crux-users" group.
> To post to this group, send email to crux-...@googlegroups.com.
> To unsubscribe from this group, send email to crux-users+...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/crux-users?hl=en.
>
>