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View Code? Open in Web Editor NEWPDV: an integrative proteomics data viewer
License: GNU General Public License v3.0
PDV: an integrative proteomics data viewer
License: GNU General Public License v3.0
Hi, I processed .d raw files with Fragpipe and wish to review the identifications.
It is not clear which raw files I should use because the data was read directly in Fragpipe and was not transformed to mzML.
Thanks,
Yishai
Dear PDV developers team,
I would like to visualize the MSfragger results for a fractionated sample. In this case I only have 1 pepxml file and 2 mzML raw spectra. How can I use PDV for this visualization? Unfortunately the PDV 1.7.3 gives an error message when I tried to import both raw files. Please see the attached image.
Thanks
Hello, how does the author use the graphical user interface?I can't call out interface.
Hi Bo, we are making some changes to the formatting of the MSFragger psm.tsv result files from FragPipe/Philosopher, and our updated tables are no longer compatible with PDV. Can you take a look at this new table?
Thank you!
Sarah
psm.tsv.zip
my command:
java -jar /share/liuqi/ganyuli/proteome/software/PDV-1.7.4/PDV-1.7.4.jar
-r combined
-rt 5
-s .
-st 1
-i tab2.txt
-k s
-o output
-a 0.5
-c 5
-pw 1
-fw 800
-fh 400
-fu px
-ft pdf
Possibly, I didn't set the corret input data format, so always appeared this error when I used the command line for visualizing maxquant results:
Exception in thread "main" java.lang.NullPointerException
at java.base/java.io.FileInputStream.(FileInputStream.java:149)
at java.base/java.io.FileReader.(FileReader.java:75)
at PDVCLI.MaxQuantImport.parseParameters(MaxQuantImport.java:1024)
at PDVCLI.MaxQuantImport.(MaxQuantImport.java:162)
at PDVCLI.PDVCLIMainClass.importFile(PDVCLIMainClass.java:669)
at PDVCLI.PDVCLIMainClass.runCMD(PDVCLIMainClass.java:389)
at PDVCLI.PDVCLIMainClass.(PDVCLIMainClass.java:229)
at PDVGUI.gui.PDVMainClass.main(PDVMainClass.java:282)
So what is the correct input data format for visualizing maxquant results by command line?
Hi,
How can I define a new modification in PDV?
Hi all,
I'm trying to test PDV (GUI) with one single mzid from MetaMorpheus (30MB).
However, as soon as I select the the file I get the warning in the title.
This seems strange to me since my machie has 128GB RAM and I'm running PDB as the following:
java -Xmx80G -jar PDV-1.7.4.jar
Even if only loading one mzML, the loading does not seem to finish.
I'm running everything on an arch linux machine to which I connect via VNC from a macbook.
Did you encounter something similar and have any idea whats going wrong?
When trying to run the example as following:
DISPLAY=:1 java -jar PDV-1.7.4.jar -r input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1_myrimatch_mzML.mzid -rt 1 -s input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML -st 2 -i input_data/spectrum_scan_number.txt -k s -o output -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf
I end up with the following stack trace:
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/manuel/Apps/PDV-1.7.4/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/manuel/Apps/PDV-1.7.4/lib/logback-classic-1.1.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
Exception in thread "main" java.lang.ExceptionInInitializerError
at com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:83)
at com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:176)
at com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:282)
at com.sun.xml.bind.v2.runtime.property.ArrayProperty.<init>(ArrayProperty.java:69)
at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.<init>(ArrayERProperty.java:88)
at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.<init>(ArrayElementProperty.java:100)
at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.<init>(ArrayElementNodeProperty.java:62)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:181)
at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:509)
at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:326)
at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:141)
at com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1157)
at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:145)
at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:236)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:186)
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:146)
at javax.xml.bind.ContextFinder.find(ContextFinder.java:348)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:446)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:409)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:313)
at uk.ac.ebi.pride.utilities.pridemod.io.unimod.xml.unmarshaller.UnimodUnmarshallerFactory.initializeUnmarshaller(UnimodUnmarshallerFactory.java:36)
at uk.ac.ebi.pride.utilities.pridemod.io.unimod.xml.UnimodReader.<init>(UnimodReader.java:35)
at PDVGUI.utils.ImportPTMsFromUnimod.parsingFile(ImportPTMsFromUnimod.java:55)
at PDVGUI.utils.ImportPTMsFromUnimod.<init>(ImportPTMsFromUnimod.java:34)
at PDVCLI.PDVCLIMainClass.runCMD(PDVCLIMainClass.java:246)
at PDVCLI.PDVCLIMainClass.<init>(PDVCLIMainClass.java:229)
at PDVGUI.gui.PDVMainClass.main(PDVMainClass.java:282)
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make protected final java.lang.Class java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws java.lang.ClassFormatError accessible: module java.base does not "opens java.lang" to unnamed module @34129c78
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199)
at java.base/java.lang.reflect.Method.setAccessible(Method.java:193)
at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:177)
at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:174)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:318)
at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.<clinit>(Injector.java:172)
... 37 more
Can you help me with getting PDV to run on a remote linux server (either ssh or vnc are okay for me)
Best,
Manuel
I have found several grammar issues while reading the PDV manual on your website. What is the best way for me to submit corrections for them?
Interesting: Yesterday I downloaded PDV to view data generated in Fragpipe, and it worked nicely. I was able to open the View>Column Selection. and added the proteinID and descriptions (these are really good for users of our proteomics core facility to browse and filter their data).
Today, I cant get Column Selection to open in both of my computers where I downloaded PDV. When I click ColumnSelection, an empty window appear where I can only read: "Column"
Any ideas?
java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
at PDVGUI.gui.utils.SpectrumMainPanel.updateSpectrum(SpectrumMainPanel.java:1477)
at PDVGUI.gui.utils.SpectrumMainPanel.updateSpectrum(SpectrumMainPanel.java:2011)
at PDVGUI.gui.PDVMainClass.updateSpectrum(PDVMainClass.java:3786)
at PDVGUI.gui.PDVMainClass.spectrumJTableKeyReleased(PDVMainClass.java:3230)
at PDVGUI.gui.PDVMainClass.access$400(PDVMainClass.java:57)
at PDVGUI.gui.PDVMainClass$5.keyReleased(PDVMainClass.java:869)
at java.desktop/java.awt.AWTEventMulticaster.keyReleased(Unknown Source)
at java.desktop/java.awt.Component.processKeyEvent(Unknown Source)
at java.desktop/javax.swing.JComponent.processKeyEvent(Unknown Source)
at java.desktop/java.awt.Component.processEvent(Unknown Source)
at java.desktop/java.awt.Container.processEvent(Unknown Source)
at java.desktop/java.awt.Component.dispatchEventImpl(Unknown Source)
at java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source)
at java.desktop/java.awt.Component.dispatchEvent(Unknown Source)
at java.desktop/java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
at java.desktop/java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(Unknown Source)
at java.desktop/java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(Unknown Source)
at java.desktop/java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Source)
at java.desktop/java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
at java.desktop/java.awt.Component.dispatchEventImpl(Unknown Source)
at java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source)
at java.desktop/java.awt.Window.dispatchEventImpl(Unknown Source)
at java.desktop/java.awt.Component.dispatchEvent(Unknown Source)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.desktop/java.awt.EventQueue$5.run(Unknown Source)
at java.desktop/java.awt.EventQueue$5.run(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.desktop/java.awt.EventDispatchThread.run(Unknown Source)
java.lang.ArrayIndexOutOfBoundsException
Hi,
I am using the newest version of PDV to visualize MSFragger output (through fragpipe) on our Windows10 desktop. I used the pep.xml and mzML files according to the manual. The files seem to be parsed by PDV but it doesn't generate the annotated spectrum. Please see he attached file. Any help will be greatly appreciated.
Thanks
Hi,
I've imported a file searched by metamorpheus, and most scans containing various modifications are not shown.
Additionally, when two peptides are identified from a single scan (mixed spectra), only one is shown in PDV.
Thanks!
David.
The following attached image shows iH ion colored green as if it was a matched b-ion. Peptide is QKNPSVIHF.
The mgf file containing the scan:
After selecting the input files for database searching, the "loading data" bar pops up but the data never loads. I am running java 18.0.1.1 and PDV 1.7.4 with Windows 11. The same data loaded easily on a laptop running Windows 10. Is there any way around this?
Thank you
The documentation says that the database search functionality can parse "MS-GF+, MyriMatch, X!Tandem, OMSSA (convert OMSSA raw result to mzIdentML format using MzidLib: https://github.com/PGB-LIV/mzidlib), Crux, Comet, Mascot, IPeak and
MSFragger." Crux is the name of the toolkit, and it contains two search engines, Tide and Comet. I tried to upload the attached Tide search results file, which ends in .txt. When I do this, the dialog box allows me to specify one of three options: PDV format, MSAmanda and Philosopher. How do I get it to read Tide format? If I select PDV format, then it says the format is not supported.
Exception in thread "DisplayThread" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
at PDVGUI.fileimport.TextFileImport.parseTextFile(TextFileImport.java:252)
at PDVGUI.fileimport.TextFileImport.access$100(TextFileImport.java:30)
at PDVGUI.fileimport.TextFileImport$1.run(TextFileImport.java:141)
When running log4j-detect on PDV-1.7.4, it identified the file PDV-1.7.4/lib/log4j-1.2.12.jar as vulnerable
That tool recommends to upgrade log4j to v2.17.1 from here
https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-core
With the fear of repeating what has already been posted as issues. I have an issue opening pepXML+mzML and/or tsv+mzML files generated using FragPipev14.0, using Fragger 3.1.1, Philosopher 3.4.13 (build 1611589727) and python 3.8.5 where DB splitting and Spec lib is enabeled.
The picture below is the files I've loaded. Here it is a tsv+mzXML combination.
When i Press Start it loads, and it never finishes.. Never.. as on this picture.
Just for info, I use PDV 1.7.1, mzML files are converted from *.d files via Proteowizard with the settings shown below.
Do you need any more information?
Hi PDV developer team,
We have been searching some o-linked enriched glyco-proteomics data using MSFragger. Can we visualize the spectra in PDV? Does PDV handle and show the diagnostic fragment masses?
Thanks
Hi,
I am using PEAKS X plus Studio to process my raw data (that are TIC acquired with an LC-ESI-Q-Orbitrap). The software succeed in doing data refinement as well as the de novo sequencing, however when the software ends the processing the peptide mapping with the PTMs doesn't appear in the output.
Do you know what could be the cause of this issue ?
Dear all,
Would be glad of any help or pointer. I downloaded PDV-1.7.1 and, seeing a pom.xml, decided to install the package by having, as I do normally, maven do the work by issuing
mvn package
I find that indeed
does not exist.
Any idea how to fix the problem? Many thanks in advance,
Achu
I am using the latest version of PDV on MacOS, and there seems to be a problem with the file selection dialog box. When I want to open a file, the dialog box starts from my home directory, but I am unable to descend into any subdirectories. I was forced to move the MGF file into my home directory in order to open it, but this seems like less-than-desirable behavior. :)
Hi,
I imported a mzml file and a MSFragger pepXML file. The data is imported and I can look at it, but I keep getting the following error while scrolling through PSMs:
Table not instantiated
java.lang.NullPointerException
At this point I have to force quit and restart. How do I resolve this?
Hi, Bo
I tried to add custom fragment ions for spectrum annotation. But didn't find a way. Is it doable with the current version of PDV?
Thanks!
Xudong
Hello, I am recieving an error while opening an interact.pepxml/mzml pair after Fragpipe search:
java.lang.NumberFormatException: For input string "17,3176"
Java version 1.8 on Windows 10
thanks for support,
Artur Pirog
Hi PDV community,
I was trying to visualize some .pepXML results and .mzXML files exported from PEAKS Studio 10.5.
However, I am receiving an error (attached image) that is preventing me to do any visualization. My computer is german and the decimal delimiters ("," for Germany) is the only thing that comes to mind...
Any suggestions for how to fix this? I was very curious to explore the visualization/annotation of PDV for peptides carrying PTMs not present in unimod.
Sincerely,
JC
I think it would be convenient if, when visualizing a single PSM, the user could provide an MGF file containing multiple scans along with something like the scan number or title to indicate which scan to visualize.
Dear developer,
Thanks for the powerful tools you developed!When i use this software in windows,i could not find a good way to export my modification spectra expediently. Could you give me a right method to solve this problem?
yours sincerely,
gaoxiang cao
Hi all,
After speaking with Nesvilab, they encouraged me to write to you guys.
So, I tried to import combined.pep.xml
with .mgf
files created by both FragPipe itself and by http://fields.scripps.edu/rawconv/ and it doesn't work (set of 9 .raw files)
The message is always:
Then I tried to upload a single file from psm.tsv
with the .mgf
from FragPipe and this works:
However, when I combine few psm.tsv
together and add multiple .mgf
files, it fails again:
Any idea, how to upload more than 1 raw file at once?
All the best!
Greets
Witek
Hi,
A mass error plot for fragments would be a very good enhancement for better peptide spectra manual quality assessment.
PDV works fast and reliable for otherwise problematic to visualize results.
Artur
Export in ONE Psm mode does not work properly. In case of pdf it generates it but with loading bar in a top of the graph
G_13_2.6100.6100.3 FileG_13_2.raw, NativeIDcontrollerType=0 controllerNumber=1 scan=6100.pdf
PNG and TIFF files are not generated. Two files are generated: .temp and .png (or .tiff). While .tmp files contain something (they have certain weight), the .png and .tiff files are empty.
Hi!
Currently using Fragpipe to run XRNAX protocol, I have a couple of questions.
Hello,
We are running the PDV-1.7.3 to open the files produced by MSFragger.
But we can only open the file called "psm.tsv". However, the data we need was stored in the "global.modsummary.tsv" or "modifications.tsv". Could you please tell me if the PDV could open such files?
Thank you in advance.
ZXY.
I have a PSM.tsv file from FragPipe/philosopher and I can load it and mzML spectra. It works well.
However, as with any dataset, the data is split into multiple pages when I load it.
Is there a way to search for a particular peptide/protein/scan etc across ALL pages?
Sort the whole dataset?
It looks like those functionalities are applied to each page independently now.
Thank you
Alexey Nesvizhskii
I tried to parse a Tide pepXML file, but failed. The error is "Failed to parse the PepXML file, please check your file." I suspect that this is because our format has changed since you first evaluated Tide's PepXML back at Crux v3.2. Can you take a look at the attached file and see if it's possible to support it, or if we need to make changes on our end?
plasmo-neighbors.trypsin-p.narrow.tide-search.pep.xml.txt.gz
MSB17171Trypsin030814.mgf.txt.gz
This is rather a feature request than an issue. It would be nice if the PSM table could be string-queried-filtered (not just sorted) by ProteinID, Entry Name and protein Description. This feature would be great for browsing big datasets.
System: Linux
java -jar PDV-1.0.0.jar --help
Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
at java.awt.Window.(Window.java:536)
at java.awt.Frame.(Frame.java:420)
at java.awt.Frame.(Frame.java:385)
at javax.swing.JFrame.(JFrame.java:189)
at PDVCLI.PDVCLIMainClass.(PDVCLIMainClass.java:173)
at PDVGUI.gui.PDVMainClass.main(PDVMainClass.java:247)
I just downloaded PDV (trying both 1.7.0 and 1.7.3). The GUI opens fine, but when I click on some of the options nothing happens, for example for database searching, denovo sequencing, and one PSM no window pops up when I click on them. Other options are fine and function as expected, including spectrum library MS data. Is there a trick to getting the database search option to function?
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