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-Proteomic%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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
