Perfect, thanks Jimmy. On Apr 7, 2017 2:51 PM, "Jimmy Eng" <[email protected]> wrote:
Comet defaults to "unknown" for both the instrument model and instrument manufacturer if neither of those are set in the input file. As I don't have any strong feelings about this, I just changed the code to report "UNKNOWN" which will be what's reported in the next release (which is way overdue). On Fri, Apr 7, 2017 at 2:34 PM, Luis Mendoza <Luis.Mendoza@systemsbiology. org> wrote: > Hi Joey, > Glad that the new Petunia worked for you. Do let us know if you find > anything amiss, since this is a pre-release version with a handful of new > (semi-tested) features. > > As for the "unknown" instrument type, I just want to make sure that you > started with the same mzML file for each of the searches. While this gets > resolved, you may want to use the -Ow option in xinteract: "[issue a] > warning instead of exit with error if instrument types between runs is > different". Let us know if this avoids the error and thus the need for > your python script. > > Cheers, > --Luis > > > On Wed, Apr 5, 2017 at 5:09 PM, Joey Davis <[email protected]> wrote: > >> Hi Luis, >> >> This is perfect, thanks so much - that fix works perfectly with comet and >> all the downstream tools. >> >> I also noticed that with our particular wiff files (generated on a SCIEX >> 5600+), comet includes a line in its xml file listing the instrument type >> as 'unknown'. In contrast, xtandem uses uppercase and lists the instrument >> as 'UNKNOWN'. This change in case causes errors with peptideprophet (and >> iprophet, I think). I have a small python script that now fixes the comet >> files to always use upper case in that entry, but just wanted to let you >> guys know; not sure if there's an easy fix on your side or if it needs to >> be standardized in the search engines. >> >> Thanks again for your help, >> joey >> >> On Wednesday, April 5, 2017 at 3:39:36 PM UTC-7, Luis wrote: >>> >>> Hi Joey, >>> >>> I have placed a .zip file (PETUNIA 5.1beta.zip) with Petunia and a >>> couple of support files here: >>> https://sourceforge.net/projects/sashimi/files/Trans-Proteom >>> ic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/ >>> >>> Once you download and uncompress, place the unzipped files as such: >>> tpp_gui.pl --> C:\TPP\cgi-bin\ >>> tpp_gui.css --> C:\TPP\html\css\ >>> filterTable.js --> C:\TPP\html\js\ >>> >>> Please make a back-up of your existing files before replacing with these >>> new ones, or you might have to re-install TPP if things go awry. >>> >>> Hope this helps, and let us know how it goes. >>> --Luis >>> >>> >>> >>> On Tue, Apr 4, 2017 at 6:17 PM, Joey Davis <[email protected]> wrote: >>> >>>> Hi Luis, >>>> >>>> That would be great - I'd love to use it even before the official >>>> release. Would it be possible to post a link to the unsupported pre-release >>>> executable? >>>> >>>> Thanks, >>>> Joey >>>> >>>> On Friday, March 17, 2017 at 3:49:06 PM UTC-7, Luis wrote: >>>>> >>>>> Hi Joey, >>>>> >>>>> No bother at all, and thanks for reporting this. We actually >>>>> identified this as a bug a couple of months ago, and have implemented a >>>>> fix >>>>> which will be part of our next release -- due in about 5-6 weeks. >>>>> I can also send you an updated Petunia executable if you'd like to use >>>>> this feature before the official release; just let me know. >>>>> Cheers, >>>>> --Luis >>>>> >>>>> >>>>> On Mon, Mar 13, 2017 at 10:23 PM, Joey Davis <[email protected]> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> Sorry to bother, but I just setup TPP on a new Windows 10computer >>>>>> where I will be keeping all of my data on D:\. For all searches, I get >>>>>> the >>>>>> error: Error - input file "XXX.mzML" not found. It appears that in >>>>>> Windows, >>>>>> in initial cd command fails if you are trying to both change drives and >>>>>> change directories as the search works if I run it from the command >>>>>> prompt >>>>>> after having switched drives to D:. It is possible to instruct Petunia to >>>>>> prepend the comet commands with a change drive command (simply D:\ && cd >>>>>> D:\xxx). >>>>>> >>>>>> Thanks, >>>>>> Joey >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "spctools-discuss" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to [email protected]. >>>>>> To post to this group, send email to [email protected]. >>>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to a topic in the Google Groups "spctools-discuss" group. 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