ReleasePlanning
From SPCTools
This page is intended to assist in release planning by tracking new feature requests/bugs/improvements etc for TPP.
Contents |
For Next Release
Planned timeline
- 4.6.3 released 7/24
- Release 4.7.0 9/15?
Completed Tasks
- IMPROVEMENT: I/we need to update pepXML Viewer to display the search scores from Myrimatch.
- (Luis) NEW FEATURE: Include support for msgfplus
Pending Tasks
- (Joe) new decoy generator doesn't know about NCBI "|" so creates funny sequence ids
- BUG: InteractParser issue reported by Jimmy https://groups.google.com/forum/?fromgroups#!topic/spctools-dev/utMNvSzJcFE
- BUG: Path bug? https://groups.google.com/forum/?fromgroups#!topic/spctools-discuss/a9LF_Y_NU_M
- (Joe) BUG: On Windows it seems to have a hardcoded path to perl so that the programs/cgi scripts fail if you put perl in another location, e.g. installing 64 bit perl which goes to C:\Perl64 instead of C:\Perl.
- (Luis) NEW FEATURE: Support of Comet in the prophets, quant, viewers
- (Luis) NEW FEATURE: Support of OMSSA in the prophets, quant, viewers
- (Joe) NEW FEATURE: updateAllPathsNoReallyThisTime.pl
- (Luis) Add support for XPRESS ppm tolerance (-a) to Petunia
- (Luis/Joe) BUG: lorikeet uses hardcoded paths to the html and javascript directories on the Apache server (e.g. ISB/js/lorikeet.js) instead of using the TPP_WEB Makefile variable.
Postponed Tasks
- IMPROVEMENT/BUG: Have the TPP installer fill in the correct paths in tpp_gui.pl when building. Warn if a program can't be found.
- (Joe&Mike) IMPROVEMENT: Upgrade X!Tandem
- BUG: any remaining issues brought up at http://www.viva64.com/en/b/0156/
- (Joe) IMPROVEMENT: Include amztpp in the distribution
- (Joe) IMPROVEMENT: Update Pwiz on the Linux side?
- (Luis) IMPROVEMENT: This one goes to "11", or in this case 10.
- Comet will output +10 charge states and this will no doubt cause trouble in TPP
- (Joe+Steve) NEW FEATURE: Bundle idConvert, Petunia page, Steven is fixing it and working with Matt
- (Luis+Joe) NEW FEATURE: SGE job submission support (so that users can finally use 100% of petunia at ISB)
- (Luis) Provide a db fmt/verifier and possibly tie this into a decoy maker?
- (Joe) Upgrade svn clients/server
Miscellaneous Ideas
- Breakout apache configuration into its own file and handle it properly on Ubuntu systems
- Confidence
So I saw again today Luis squirming under the question what is the “confidence” metric in ProteinProphet. It seems like it’s just confusing people. I suggest we sneak in a quick fix before the release of 4.6.3 to add an option to enable the printing of the confidence metric and that option be OFF by default. So that people who still want to use it can by setting an option, but by default most users will not be troubled by this.
- NEW FEATURE: PEFF support in TPP. (Need to define what this means).
- 64 bit version of TPP? mingw-64 is stable now. http://mingw-w64.sourceforge.net
- Feature thought - Transition petunia from using tandem.params.xml to tandem.params. While I understand in Petunia its historically been called tandem.params.xml and I'm loath to change this because of the impact. Why? For two reason. The first is I expect very shortly we'll be shipping at least one more search engine with TPP (comet) and it doesn't have a "comet.params.xml" file. Secondly on regis we've always (since I've joined ISB at least) called it tandem.params. Now I don't pretend to think we should make our users conform to us, I do however think we need to recognize that internally we support a large array of search engines and we've taken to naming all of the parameter files as <search>.params. To name this omssa.params.xml, inspect.params.xml, etc would be incorrect as these aren't always in xml format. Now I guess for those formats that aren't in xml we could create one but I don't think that's a great approach. Instead I propose following what I've done on regis, which is to use the native parameters file format when possible and in the cases were there isn't one (just command line parameters) use a very simple format that consists of just including all of the command line parameters. Alternately I guess we could just recognize both tandem.params and tandem.params.xml
- Better support for viewing/outputting N15 experiments. Sequences are hard to read (modification every base) and makes the xml huge.
List of suggested TPP new features, improvements, fixes, etc.. to be cherry picked for upcoming releases.
- Add ASAPRatio option to use WaveletQuant in Petunia
- Verify that xinteract can deal with this option (-w)
- Petunia: option to run xinteract jobs as separate (instead of combining into a single analysis)
- Figure out installation of PepC (B.Pratt?)
- Make sure new installation of QualScore works on Windows
- Output more significant figs for Protein Prophet weight (rounding error on 0.49 and 0.50)
- Fix precursor charge column (only 1st letter displayed) and miscalculation of the # of unique peptides in EXCELPEPS
- EXCELPEPS appears to be broken; just remove it?
- Resolve Andreas issue with Tandem2XML
- Write (TPP) software version used in pepXML, protXML, etc
- Silence/catch errors on the *Prophet models generation when no data (e.g. "empty y range")
- Zhi has been experiencing a bus error one large operation with SpectraST
- There is a was a reported bug by Henry with mzParser
- Add commandline option to generate EXCEL output of pepXML files
- Issue with MzXML2Search converting older mzXML files to mgf. Randomly fails on the same file.
- Missing javascript file for table filtering in Petunia (only affects Linux installations)
- I encountered a small problem when using the new TPP. In the prot.shtml view, pink color coding of NxS/T motifs does not work anymore when checking the box. Also, I always liked the "464 peptides with NXS/T motif, 690 total peptides, 658 unique stripped peptides"info at the bottom of the page (as it gives us an immediate idea of how nicely a glyco experiment worked) but this is not displayed correctly anymore.
- Included Terry's latest version of Inspect2PepXML.py for patching inspect installations
Legacy Items
Fix iProphet models page ("performance" models are missing)
- Add "Bruker" files option to msconvert in Petunia
- Fix pepxml2html (View Peptide hits) peptide link for SpectraST results
- peptidexmlhtml2 : does not work with AA highlighting option (mark_aa=)
- Add some filtering options to Pep3D (specifically: view only +1 ions)
- Add QuickMod to speclibs page?
- retire getSpectrum -> use readMzXML
- incorporate psm2pdf
- include t2d support(?)
- Petunia: option to convert to mzXML using msconvert
- Petunia: launch all external links in blank/target window
- Reindex mzXML: new file with old name; rename old to: old-index or some such
- Petunia: option to run xinteract jobs as separate (instead of combining into a single analysis)
- Petunia: select pep.xml files only for input to Decoy Models pages
- Petunia: auto cd to dir and strip out full path if all files in same dir (shorten command line)
- Petunia: rename Mascot file on download
- Move /tmp/ directory under tpp-bin (Windows)
- Petunia: Add TPP version check (ping server) --> usage stats
- Petunia: add full filters to msconvert(??)
- Petunia: change tab graphic when jobs are done?
- PepXMLViewer: implement "preferences" tab: choose ions series, spectrum viewer, etc... ?
- PepXMLViewer: no pep-pro probability link in iProphet results
- Libra also needs some love (ability to curate ratios would be a great start...)
== From Henry (perhaps he already checked this in?) :
Following up on this discussion, I would like to propose the following. (This is not urgent since our course doesn't use OMSSA or any of the newly-supported engines, so it doesn't need to be in the release soon.)
1. Change xinteract to run RefreshParser before PeptideProphet.
This takes care of the protein name issues for OMSSA, and makes sure that the NTT and NMC fields are there and calculated correctly for PeptideProphet. Some search engines don't fill in those fields and cause PeptideProphet to crash.
The flip-side is mainly inefficiency. If the user decides not to keep all search hits regardless of probability (i.e. not specifying -p0), then this means RefreshParser unnecessarily refresh a bunch of wrong identifications that won't be in the final pepXML file anyway. But then again, given that nowadays PeptideProphet often relies on the protein name (whether it's a DECOY or not), it seems safer to ensure that the protein names are right -- even for the wrong hits -- before we run PeptideProphet. Also, with the new implementation, for most files RefreshParser is so fast that I don't think it will make much difference in running time anyway.
If the user doesn't want to refresh, he/she can always turn off RefreshParser (-nR option).
2. Have InteractParser detects if the search engine is OMSSA, and if so, apply the fix_pyro_mods_ option automatically.
This goes without saying. The only thing is the user doesn't have to turn on the option manually. I don't know if other engines have the same problem. If so, it's easy to add them to the list.
