I managed to get it to work with both XPress and ASAPRatio values. Just
added the line:
asap_mean = p.xpath('n:analysis_result/n:XPressRatio', namespaces = NS)[0
].get('ratio_mean')
at line 78 of the ProXML2Csv script, along with variables in the required
spots to hold and output the ratios.
If you need more detail about what I changed let me know and I will post it
here.
Chris
On Sunday, October 20, 2013 8:24:32 PM UTC+2, chr12is wrote:
>
> It seems that the XPRESS values that one would like to parse out, such as
> the mean, deviation, and count are not defined in the protXML schema, and
> are therefore not defined in the namespace. Is it still possible to parse
> them from the file?
>
> Chris
>
>
>
> On Sunday, May 26, 2013 8:41:56 PM UTC+2, chr12is wrote:
>>
>> Hi All,
>>
>> I seem to be having an issue with getting my output in excel format. I am
>> currently using TPP 4.6.2 on a linux cluster with CentOS.
>>
>> I generated my output.xml file using xinteract (running protein prophet
>> as part of this command). The resulting output.prot.xml file from xinteract
>> contains all the information I am interested in, including XPRESS ratios.
>> However, I now want to take my result file elsewhere to do some analysis,
>> such as R. To do this I would like to run some perl scripts on it, but
>> parsing an XML file with perl is a bit tedious. As such, I would like to
>> have it in Excel format so I can get the tab or comma delimited versions.
>>
>> I have tried to get the excel file using two options. This first is using
>> the 'protxml2html.pl' script and passing it the excel option. It seems
>> the XPRESS ratios are lost during this conversion. The html version doing
>> this also does not contain the XPRESS ratios.
>>
>> The second option is to re-run protein prophet on the resulting
>> interact.xml file and pass it the XPRESS option. It seems to work ok, but
>> when it gets to XPRESS, and says 'importing XPRESS ratios', it completes
>> almost instantly, and doesn't write the ratios to the file...otherwise the
>> file is ok.
>>
>> I am working on a cluster purely through command line, so a fix that is
>> based on this is desirable.
>>
>> Thanks for any suggestions you may have!
>>
>> Regards,
>> Chris
>>
>
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