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 <joeyda...@gmail.com> 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 <joey...@gmail.com> 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 <joey...@gmail.com> 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 spctools-discu...@googlegroups.com. >>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>> 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 spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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. 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