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Alphatims export selection - need help #192
Replies: 3 comments · 8 replies
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Hey @witszymanski . If you just remove the comma, it does work on my system: |
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Hi! Thanks for the fast reply. So indeed it was just the coma. I get still some errors though. If I run it on the .d folder, I get this:
If I do it on the .hdf file generated before by Alphatims, i get this:
Any ideas? |
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Good to hear it works (at least it starts...)! For the first issue, I am not completely sure. I expect it to be a memory issue, which should be fixed in v1.0.0 due to the usage of mmaps instead of RAM. You can test this one out by updateing to the latest development branch, which is not officially released just yet with: For the second issue with jinja you are in more luck. Probably this will be fixed by downgrading jinja with |
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So, in order to make it work, I had to do all 3 things mentioned above :) I was doing it step by step.
Question: Thanks for the help!! If this will work how I hope, it will be of a great help to generate some standard reporting outputs! |
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Hmm, your update from the dev branch still uses Alphatims 0.3.2. My bad, you probably should have appended a Funnily enough, I have actually not implemented a TIC export before even though this is most likely a simple copy-paste from the nbs tutorial to the CLI. If you want to help and make a PR, feel free to try it out and implement it (git pull from dev branch first). Otherwise I will probably get to this in a later release, but I have no idea about that timeline... |
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Another side note: if you use v1.0.0 and make an hdf first, this should be significantly faster to do a data selection you have done now (seems to take 629s, probably can be done 100 times faster if you have an hdf format) |
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But you still need a lot of time to create the hdf files ;) Anyway, so it means that in the current state, I can't export the TICs right? To be honest, I am mainly a mass spectrometrist and not a bioinformatician (only partly so, because of the necessity), so I would have no clue how to implement this in the code myself :( |
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From hdf:
|
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Slower than I expected it (I probably can speed that up a little more), but at least you don't have to get a coffee while waiting anymore;) |
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Yes, but that conversion is a one time thing. I presume you want to do more with your data than just visualize a single plot, especially since you already mention you want a TIC as well, and a second plot means reading in the data at least twice in the current implementation. Yes, you are right that currently exporting the TIC from CLI is not a (convenient) option. In principle you can select all data and export an XIC, which amounts to the same thing. Realistically this will probably kill your memory though... No worries about the programming skills, I'll see if I can get this on my short-term todo list without making any promises just yet;) |
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I tried this, it does kill everything :D Thanks for the help, and I'll follow new developments here! |
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Hi all!
I am a bit lost in the CLI of the Alphatims and I am sure it's just trivial, but I can't make it work. So In general I want to recreate this:
by using a command line and save png on the drive.
I was trying to run this:
I was trying different things (brackets, spaces etc.) with the float argument, but nothing is working. How should it look like?
I'd be grateful for the help!
Greets
Witek
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