Hi Matt, Sometimes when you have to explain stuff like this it is a good indication that the interface could be made simpler for the user. In this case, I think msconvert should probably check whether a WIFF file has more than one sample entry, and just use the file without any sample name without any disambiguation when only one entry exists. Falling squarely under the software principle: make the complex case possible, but keep the common case simple.
--Brendan On Jan 19, 9:38 am, Matthew Chambers <[email protected]> wrote: > Hi Gautam, > > This is because a single WIFF can contain multiple "samples", each of which > translate to a separate > mzML document. Each document can't be named the same, so we append the > "sample name", or if that's > not unique, we add a duplicate count like "(2)". An override was recently > added to msconvert for > setting the output filename, but I expect that would explode for a > multi-sample WIFF file (which are > not at all uncommon). > > -Matt > > On 1/19/2012 8:41 AM, Gautam Saxena wrote: > > > > > > > > > Hi, > > > When using msconvert on ABI wiff files, it seems to suffix the > > converted output file with the word "-Sample". Is this intended? This > > suffixing does not occurr with Thermo .raw files, so why should it > > occur with wiff files? Here's an example output: > > > =========================== > > R:\programs\windows_programs\msconvert\msconvert.exe --filter "msLevel > > 2-" --mzXML --64 --mz64 --inten32 F:/JHU_NHLBI_MS_FILES/ > > Melanies_iTRAQ_data/wiff_files/Fraction1/Fr1_1.wiff > > > format: mzXML (Precision_64 [ 1000514:Precision_64 > > 1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None) > > indexed="true" > > outputPath: . > > extension: .mzXML > > contactFilename: > > > filters: > > msLevel 2- > > > filenames: > > F:/JHU_NHLBI_MS_FILES/Melanies_iTRAQ_data/wiff_files/Fraction1/ > > Fr1_1.wiff > > > processing file: F:/JHU_NHLBI_MS_FILES/Melanies_iTRAQ_data/wiff_files/ > > Fraction1/Fr1_1.wiff > > writing output file: ./Fr1_1-Sample.mzXML > > ========================= > > > The version of msconvert being used is shown below: > > > ========================================== > > W:\lab1\jsmith_university_edu\Workflow_Outputs\DJ8C>R:\programs > > \windows_programs\msconvert\msconvert.exe --version > > unknown option version > > Please report this error to [email protected]. > > Attach the command output and this version information in your report: > > > ProteoWizard release: 2.2.2997 (2011-9-19) > > ProteoWizard MSData: 2.2.2997 (2011-9-19) > > ProteoWizard Analysis: 2.2.2976 (2011-9-14) > > Build date: Sep 19 2011 17:00:29 > > =========================================== -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
