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RNA-FRETools / MASH-FRET

MATLAB package to analyze single-molecule FRET data
https://rna-fretools.github.io/MASH-FRET/
GNU General Public License v3.0
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MASH-FRET bug report #66

Closed Befazl closed 4 years ago

Befazl commented 4 years ago

Describe the bug

To Reproduce Steps to reproduce the behavior:

  1. Go to 'Tools'
  2. Click on bin time axis and define a new bin time (e.g. 0.1 s)
  3. Choose source folder of exported ASCII files
  4. See error

Error Code Error with file n°:279, L14_10mM_autotag_G045_2ndsort_mol9of279.txt Unrecognized function or variable 'pname_out'. in function: binTrajFiles, line: 88

Expected behavior A new folder with ASCII files of the binned traces Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

Additional context Add any other context about the problem here.

Your contact besim.fazliji@chem.uzh.ch

Befazl commented 4 years ago

Describe the bug

Bin time axis: I have tried binning the time axis via using this separate function: binTrajFiles.zip Running the function, you can choose the source folder and it also generates a "binned" folder, but it does not generate the binned files and it shows an error.

To Reproduce Steps to reproduce the behavior:

• Open Matlab • Open the function binTrajFiles.m and run (important: add to path) • Make sure that only unstructred files are in the folder of your choice (note: the files should not be restructured, all exported ACII files are not restructured, can be easily figured out by opening one file and look if there is one column per excitation wavelength, the files are not restructred) • Editor window: copy line no 5 to the command window (the whole path without the %) binTrajFiles(['C:\Besim\06_data smFRET\L14_17_15_mW\L14_10mM\L14_10mM_merged\L10_10mM_2nd sort_all\traces_ASCII'], 0.10175); 0.1075 is the binning time here • Change the path to the path you want • binTrajFiles(['D:\0100_Projects\PJ001_smFRET_invivo\016_RawData\0113_smFRET\20170809\all_20170809_25C\20170809_25C_all'], 0.10175); • Press enter or Run -> a new folder called binning is created • See error

Error Code Error with file n?:1, L14_10mM_autotag_G045_2ndsort_mol100of279.txt Index exceeds the number of array elements (0). in function: arrangeColumns, line: 180

Expected behavior A new folder with ASCII files of the binned traces

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information): OS [Windows 10] Matlab Version [2019b] MASH-FRET Version [1.1.2, prev. commit: 86500f0]

Additional context Add any other context about the problem here.

mca-sh commented 4 years ago

Hello Befalz and thank you for reporting these bugs. I've just made the appropriate corrections in the branch MASH-code-16. You can download the new version of MASH-FRET here: https://github.com/RNA-FRETools/MASH-FRET/archive/MASH-code-16.zip. Please tell me if it works for you too so I can close/not the issue.

Also I have one comment on the steps to reproduce in your second report: the folder path comes in the second argument of the function, such as: binTrajFiles(0.10175, ['D:\0100_Projects\PJ001_smFRET_invivo\016_RawData\0113_smFRET\20170809\all_20170809_25C\20170809_25C_all']);

Befazl commented 4 years ago

Hi mca-sh! Thank you very much for the quick response and fix of this issue! It works now perfectly. :)

Befazl commented 4 years ago

Hi Mélo,

Thank you again for the fast fix of this issue :) Really appreciate it!

Could you tell me how the binning is calculated in detail? My initial thought was that, when I am binning the time axis, all counts in the defined bin are summed up and displayed, but apparently it is not. Possibly I just don't get how it is calculated. I was looking also in the documentation, but I didn't find anything.

E.g. in the following trajectory:

The non-binned data has a time res. of 30 ms, and in the traces you see that the intensity of counts is around 3000 counts:

When I bin the data to 90 ms, I expected to have 9000 counts in the y-axis, but it is still 3000:

Best wishes from rainy, rainy Switzerland :)

Besim

-----"Mélodie Hadzic" notifications@github.com schrieb: ----- An: "RNA-FRETools/MASH-FRET" MASH-FRET@noreply.github.com Von: "Mélodie Hadzic" notifications@github.com Datum: 14.06.2020 13:59 Kopie: "Befazl" besim.fazliji@chem.uzh.ch, "Author" author@noreply.github.com Betreff: Re: [RNA-FRETools/MASH-FRET] MASH-FRET bug report (#66)

Hello Befalz and thank you for reporting these bugs. I've just made the appropriate corrections in the branch MASH-code-16. You can download the new version of MASH-FRET here: https://github.com/RNA-FRETools/MASH-FRET/archive/MASH-code-16.zip. Please tell me if it works for you too so I can close/not the issue. Also I have one comment on the steps to reproduce in your second report: the folder path comes in the second argument of the function, such as: binTrajFiles(0.10175, ['D:\0100_Projects\PJ001_smFRET_invivo\016_RawData\0113_smFRET\20170809\all_20170809_25C\20170809_25C_all']); — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

mca-sh commented 4 years ago

Hi Besim! Sorry for the so-formal replay on Github: I never know if you will feel offended if I get too familiar on internet so I prefere to keep it anonymous ;) Indeed, the counts are averaged and not summed up, this should be corrected (though it does not make a difference of FRET and Stoichiometry values). However, going through the code I realized that the binning is not done correctly: after binning, the starting points of red and green axis are still shifted by the old time bin. I will re-adjust this today and come back to you when it is done!

Le mar. 16 juin 2020 à 11:16, Befazl notifications@github.com a écrit :

Hi Mélo,

Thank you again for the fast fix of this issue :) Really appreciate it!

Could you tell me how the binning is calculated in detail? My initial thought was that, when I am binning the time axis, all counts in the defined bin are summed up and displayed, but apparently it is not. Possibly I just don't get how it is calculated. I was looking also in the documentation, but I didn't find anything.

E.g. in the following trajectory:

The non-binned data has a time res. of 30 ms, and in the traces you see that the intensity of counts is around 3000 counts:

When I bin the data to 90 ms, I expected to have 9000 counts in the y-axis, but it is still 3000:

Best wishes from rainy, rainy Switzerland :)

Besim

-----"Mélodie Hadzic" notifications@github.com schrieb: ----- An: "RNA-FRETools/MASH-FRET" MASH-FRET@noreply.github.com Von: "Mélodie Hadzic" notifications@github.com Datum: 14.06.2020 13:59 Kopie: "Befazl" besim.fazliji@chem.uzh.ch, "Author" < author@noreply.github.com> Betreff: Re: [RNA-FRETools/MASH-FRET] MASH-FRET bug report (#66)

Hello Befalz and thank you for reporting these bugs. I've just made the appropriate corrections in the branch MASH-code-16. You can download the new version of MASH-FRET here: https://github.com/RNA-FRETools/MASH-FRET/archive/MASH-code-16.zip. Please tell me if it works for you too so I can close/not the issue. Also I have one comment on the steps to reproduce in your second report: the folder path comes in the second argument of the function, such as: binTrajFiles(0.10175, ['D:\0100_Projects\PJ001_smFRET_invivo\016_RawData\0113_smFRET\20170809\all_20170809_25C\20170809_25C_all']); — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/RNA-FRETools/MASH-FRET/issues/66#issuecomment-644642616, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABW5THB6SJTX7WXAKSS7OALRW4Z53ANCNFSM4N4DPXUQ .

Befazl commented 4 years ago

Hello mca-sh!

Thank you for the explanation and the fix! I have received your newest version [1.1.2, prev. commit: 1ed721a] and tried the binning again.

Unfortunately, the binning was not possible. You find the description similar to the initial one below. Thanks again for your help and explanation!

Describe the bug

Bin time axis: I have been trying to bin the time axis of exported ASCII files from a MASH file. It is possible to define a new bin time in the first pop-up, and also to select the source folder where the ASCII are stored and to run, MASH does not save any files and the error showed below is coming up. To Reproduce Steps to reproduce the behavior:

Go to 'Tools' Click on bin time axis and define a new bin time (e.g. 0.1 s) Choose source folder of exported ASCII files See error

Error Code Error with file n°:1, L14_10mM_autotag_G045_2ndsort_mol100of279.txt Undefined function 'binData2' for input arguments of type 'double'. in function: binTrajFiles, line: 144

Expected behavior A new folder with ASCII files of the binned traces Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

OS [Windows 10] Matlab Version [2019b] MASH-FRET Version [1.1.2, prev. commit: 1ed721a] Additional context Add any other context about the problem here.

mca-sh commented 4 years ago

Oh my.. I forgot to rename the function within the file. Ok NOW it should be fine: https://github.com/RNA-FRETools/MASH-FRET/archive/MASH-code-16.zip.

Befazl commented 4 years ago

Hello mca-sh! Now it works perfectly. Thanks again!