#227 Add --stop-after switch to print-processed-spectra

[William S Noble]

Here is the documentation for the new switch:

--stop-after <step> - Stop after the specified pre-processing step. The full series of steps are discretize, remove-precursor, square-root, remove-grass, ten-bin, xcorr. The default value is xcorr.</step>

[Kaipo]

Here is a patch that adds the switch.

[Kaipo]

I ran print-processed-spectra with each of the steps on a test ms2 file, here are the outputs.

[William S Noble]

Kaipo,

Thanks for doing this so quickly. I didn't do a code review yet, but I did plot the sample spectra that you created. Please take a look at this URL:

http://noble.gs.washington.edu/~wnoble/proj/crux-projects/2010tinkering/results/results.html

Scroll down to the bottom to the 29 January entry, and you'll see that something seems to be amiss with the 10-bin normalization. It looks like it's doing something closer to 1451-bin normalization! Can you look into this?

Also, I think it would be a good idea to create a series of cucumber tests based on these examples (once you figure out what the problem is).

Bill

[Jeff Howbert]

Hi Bill, Kaipo,

I looked at Bill's plots, and I don't see any obvious problem with the 10-bin normalization. The plots all have around 8 or 9 peaks with intensity = 50, which is what you expect.

Also, as regards the window for removal of the precursor ... when I started working with the Crux code base about 3 years ago, it was +/- 15 Th. I know there was an intention at some point to change it to +/- 1.5 Th, but I don't know whether the change was implemented or made it into trunk. Best check the code itself.

Jeff

On Fri, 30 Jan 2015, William S Noble wrote:

Kaipo,

Thanks for doing this so quickly. I didn't do a code review yet, but I did plot the sample spectra that you created. Please take a look at this URL:

http://noble.gs.washington.edu/~wnoble/proj/crux-projects/2010tinkering/results/results.html

Scroll down to the bottom to the 29 January entry, and you'll see that something seems to be amiss with the 10-bin normalization. It looks like it's doing something closer to 1451-bin normalization! Can you look into this?

Also, I think it would be a good idea to create a series of cucumber tests based on these examples (once you figure out what the problem is).

Bill

---

** [issues:#227] Add --stop-after switch to print-processed-spectra**

Status: open
Milestone: Crux v2.0
Created: Thu Jan 29, 2015 08:46 PM UTC by William S Noble
Last Updated: Fri Jan 30, 2015 12:12 AM UTC
Owner: Kaipo

Here is the documentation for the new switch:

--stop-after <step> - Stop after the specified pre-processing step. The full series of steps are discretize, remove-precursor, square-root, remove-grass, ten-bin, xcorr. The default value is xcorr.</step>

---

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cruxtoolkit/issues/227/

To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

[William S Noble]

Sorry, Jeff, we had continued this thread outside the issue tracker and resolved various issues. The upshot is that there was nothing wrong with Kaipo's code -- I was just stupidly plotting many spectra at once. The 15 versus 1.5 thing I had double checked with Kaipo last week, and it has indeed been changed to 15 in tide-search. That change had not been propagated to this code, but that is now fixed in the subsequent patch that Kaipo sent me.

[Kaipo]

Committed in r16633