Hi Jimmy, You are right, the appended index no. is indeed interfering. It's now working and i think all the associated files (.mzXML ; .mgf ; .dat ; .tgz ; .pep.xml) should all have the same filenames. It's not sufficient just to ensure that the filepaths are consistent. I don't know how the tgz file works but apparently, when i renamed the .tgz and .pep.xml files to the same filenames as the mgf and mzXML and .dat files, everything clicked.
Thanks a million for your help! Bernt On Jul 11, 2:35 am, Jimmy Eng <j...@systemsbiology.org> wrote: > Bernt, > > If the index number is attached to the filename and somehow carried > through to the pep.xml file and URL link, that would be a problem. Make > sure that's not the case. > > The data to generate the spectral display typically comes from the mzXML > so just make sure the base_names in the resulting pep.xml files match up > to the full path mzXML file names (without the .mzXML extension). > > If you checked everything and the appended index number somehow isn't > part of the spectral display URL, reply with the value of one URL and > list the full path name of the corresponding mzXML file. For the URL, > the important bit is just the value of Dta="???". > > - Jimmy > > Bernt wrote: > > Hi Jimmy, David, > > > Thanks for the advice, I tried removing the .raw and .d from the > > extensions and changed all occurrences of the extensions in > > the .tandem files accordingly. It worked. They must be interfering > > with the file string recognition. > > > Yet when I tried the same thing for Mascot .dat files converted to > > pep.xml (I removed the .mgf extension and even the ".d" hex string in > > the .dat files) but it doesn't work (the url points to the > > generated .tgz file, but I can't view it). I have gotten rid of all > > symbols in the file names including "_" and then manually traced the > > connections all the way to the mzXML files, and everything seems in > > order. The last thing i can think of is the length of the filename > > (Mascot search generates an index no. (e.g F065672 and attaches to the > > filename). Do you think there might be something else I have missed > > out? > > > Bernt > > > On Jul 7, 2:22 am, Jimmy Eng <j...@systemsbiology.org> wrote: > >> Bernt, > > >> The good news is that you shouldn't need to re-run Tandem searches to > >> address this problem. > > >> The easiest way that I can think of to help you is to show you the > >> convention of file names, base_name attributes, and paths that the tools > >> typically expect/generate. > > >> directory of data: > >> c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/ > > >> file name of one example mzXML: > >> c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/HUOL05B01.mzXML > > >> file name of Tandem search: > >> c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/HUOL05B01.xtan.xml > > >> file name of corresponding pepXML file: > >> c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/HUOL05B01.pep.xml > > >> msms_run_summary base_name attribute in that pepXML file: > >> <msms_run_summary base_name="./HUOL05B01" > > >> msms_run_summary base_name attribute in the combined/xinteracted > >> interact.pep.xml file: > >> <msms_run_summary > >> base_name="c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/HUOL05B01" > > >> In your example below, you seem to carry a ".raw.tandem" extension > >> through everything that's a big part of the problem. After all the > >> tools are run and the URL is generated for the spectral viewer, some > >> part of this extension then is incorrectly expected to be part of the > >> mzXML file name. > > >> Digest the above and see if it helps. If I were you, in addition to > >> doing the text replacement (that I presumed you did correctly), I would > >> rename your Tandem search files (.raw.tandem) based on our convention > >> above and re-run analysis. If the spectral viewing still fails, report > >> back: > >> - directory data is in > >> - an example spectrum URL as you did > >> - full path name of mzXML file for that example spectrum > >> - msms_run_summary base_name attribute value > >> - full path name of the pep.xml file > > >> And instead of "HUOL05B01.*" in my example above, it's perfectly fine to > >> have "HUOL05B01.raw.*" if that's how you have things setup. Just as > >> long as everything is consistent. To follow-up on David's reply, I > >> believe periods (.) in filenames are fine. > > >> Good luck. > > >> - Jimmy > > >> Bernt wrote: > >>> Hi, > >>> I would like to continue an old thread: > >>>http://groups.google.com/group/spctools-discuss/browse_thread/thread/..., > >>> which has already been taken off. > >>> My problem is similar, but I have tried my best to verify that all the > >>> places referring to the raw data "path" are consistent, as advised by > >>> Jimmy in the thread. What I did was: I made a Tandem DB search at one > >>> folder level (e.g. c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/P00158), > >>> generating a set of .raw.tandem files. But later, for the reason of > >>> trying to combine 529 mzXML files together from separate folders, I > >>> moved all the mzXML and associated .raw.tandem files to another folder > >>> level (c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/). > >>> I know of this spectra viewing problem if the files were relocated, so > >>> I used a text replacing application to ensure that all .raw.tandem > >>> and .raw.tandem.params files with the string "c:/Inetpub/wwwroot/ISB/ > >>> data/OC/OGEmRPTD10/P00158" were replaced to "c:/Inetpub/wwwroot/ISB/ > >>> data/OC/OGEmRPTD10/". Only then I generated the .raw.tandem.pep.xml > >>> files from the modified .raw.tandem files and then the > >>> interact.pep.xml file. > >>> But the error still persists: command "C:\Inetpub\tpp-bin\tar.exe -tzf > >>> c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > >>> HUO00159S00168GL05B01.raw.tandem.pep.tgz "*HUO00159S00168GL05B01.raw. > >>> 0659.0659.3.dta" > /dev/null" failed: Operation not permitted Error - > >>> cannot read spectrum; tried direct .dta, from mzXML/mzData and > >>> from .tgz > >>> Below is an example of a spectra path that I tried to track: > >>> Spectra URL = > >>> &Dta=c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > >>> HUO00159S00168GL05B01.raw.tandem.pep/HUO00159S00168GL05B01.raw. > >>> 0660.0660.2.dta& > >>> Interact.pep.xml file = > >>> <interact_summary filename="c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > >>> OGEmRPTD10_Tandem_interact.pep.xml" directory="C:/Inetpub/wwwroot/ISB/ > >>> data/OC/OGEmRPTD10"> > >>> <inputfile name="HUO00159S00168GL05B01.raw.tandem.pep.xml"/> > >>> <msms_run_summary base_name="c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > >>> HUO00159S00168GL05B01.raw.tandem.pep" > >>> <search_summary base_name="c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > >>> HUO00159S00168GL05B01.raw.tandem.pep" > >>> <parameter name="spectrum, path" value="c:/Inetpub/wwwroot/ISB/data/OC/ > >>> OGEmRPTD10/HUO00159S00168GL05B01.raw.mzXML"/> > >>> HUO00159S00168GL05B01.raw.tandem.pep.xml file = > >>> <parameter name="spectrum, path" value="c:/Inetpub/wwwroot/ISB/data/ > >>> OC/OGEmRPTD10/HUO00159S00168GL05B01.raw.mzXML"/> > >>> Sorry for this long and unreadable email, but I really don't know what > >>> else I might have missed out, and I would hate to redo the Tandem > >>> search for 529 mzXML files. Would really appreciate some suggestions > >>> and advice. Thanks in advance! > >>> Bernard --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
