Comments (18)
Sorry, I can't see you picture. Could you share it again?
from pdv.
from pdv.
Hi there,
Here is a bug to export batch spectra. I will fix it in next version.
I noticed you only need one spectra. Could you please try this way to export it? Click the Export in the toolbar.
Please let me know if it doesn't works.
Kai
from pdv.
By the way, you can open PDV directly inside FragPipe right now. It will provide more information than standalone version.
from pdv.
Hi,
It worked when i exported a single spectrum according to your instructions, but i actually wanted to export the whole batch so it would be really great if you could fix the bug. And thanks for the tip about Fragpipe, will try it out.
BR Per
I actually wanted to export the whole batch
from pdv.
OK. I will try to fix it this week. Will let you you after updating the release.
from pdv.
Great, thanks, Btw, i have noticed that it can take very long time to load big datasets. Any tips on how to speed this up?
from pdv.
I optimized some steps in FragPipe version, but I don't have time to update the codes here. Could you try if it helps? And the batch export function in FragPipe is locked. I will test and open it soon.
from pdv.
OK, I will try.
from pdv.
Hi,
I just updated the package. Could you try it?
https://www.dropbox.com/s/d0qmm08luix0gcv/FP-PDV-1.0.3.jar?dl=0
Enter FragPipe folder and replace FP-PDV-1.0.3.jar with this new one:
There is a button to export selected spectra:
This function is still under testing. Please let me know if you have any issues. Or you can open a new issue under FragPipe respositry.
Kai
from pdv.
It takes VERY long time to load big datasets into PDV (for example psm.tsv from fragpipe). Any tips on how this can be speeded up?
from pdv.
As I showed in the previous post, you could try to open PDV inside FragPipe using the new package I shared with you. You don't need to import psm.tsv by yourself. After searching, click the button.
https://www.dropbox.com/s/d0qmm08luix0gcv/FP-PDV-1.0.3.jar?dl=0
It will increase 5-10X speed. Let me know if you have difficulty running it.
Kai
from pdv.
I have tested also to use PDV inside Fragpipe with the file you sent to me. It works for small datasets but it still takes very long time to open big datasets.
from pdv.
What's the raw file type? And how many raw files do you have?
from pdv.
from pdv.
Thanks, @anesvi! After changing mgf to mzml in the next version, we could open it much faster. I am testing that part. @perhag972 sorry for the inconvenience. I will send you a pre-release version once I finish testing.
from pdv.
It is 42 rawfiles from timstof data converted to mgf file of ca 5 GB each processed in fragpipe
from pdv.
I see. Will let you know if I have any updates.
from pdv.
Related Issues (20)
- Issue with coloring of i* and r* ions. HOT 2
- batch export modification spectra HOT 3
- Viewing TIMS ToF data from Fragpipe HOT 7
- PDV txt format input HOT 1
- PDV txt format input HOT 2
- Sequence in annotated figure
- how to visualize maxquant results by using PDV command line ? HOT 5
- Mass error column issue
- Color issue in spectrum annotation HOT 1
- Color issue - modification
- font size/distance issue
- Ion table - neutral loss
- Saving files on PDV from Fragpipe HOT 1
- Support for MaxQuant 2.4.2.0? HOT 4
- Exception in thread "DisplayThread" java.lang.NullPointerException HOT 4
- a question about exporting b, y ions of selected spectra HOT 6
- Difficulty with identifying phosphopeptides HOT 1
- FragPipe/DIA-Umpire HOT 2
- Java version HOT 2
- Exporting report doesn't work
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. πππ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pdv.