Great, glad it's working for you and hope the modifications weren't too
difficult to figure out.
On Monday, October 21, 2013 1:16:30 AM UTC-7, chr12is wrote:
>
> 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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