help with new Python syntax of new version

[larsyunker]

Hi folks, I had been using IsoSpecPy in my python mass spec project and haven't run the test in a little while. It looks like you've changed the imports without including documentation on how I should update my code to support your new structure. I see that in IsoSpecPyOld you discourage users from importing from that module, but it's unclear to me which functions I should be importing instead since the package structure has changed so significantly.

Currently my code is structured like so:

import numpy as np
from IsoSpecPy.IsoSpecPy import IsoSpec

iso_spec = IsoSpec.IsoFromFormula(
    molecular_formula,
    cutoff=user_threshold_value,
)
configurations = iso_spec.getConfs()
masses = configurations[0]
abundances = [np.exp(val) for val in configurations[1]]
... do other things with the masses and abundances

Since there are no docstrings for classes in the new IsoSpecPy module, it's unclear how I would accomplish this workflow with the new package structure. Could you please provide some guidance as to which things I should be importing or how I should be changing my code?

[MatteoLacki]

Hi,

Now it works like this

import IsoSpecPy as iso

minimal peak height

minimal_peak_height = 0.0001 spectrum_thr = iso.IsoThreshold(formula="C254H377N65O75S6", threshold=minimal_peak_height) list(spectrum_thr.masses) # you don't have to convert, but to see the output it helps

print(spectrum_thr.masses[0]) # this also works

list(spectrum_thr.probs)

you can also iterate

for mass, prob in spectrum_thr: print(mass, prob)

total probability threshold

total_prob = .999 spectrum_lay = iso.IsoTotalProb(formula="C254H377N65O75S6", prob_to_cover=total_prob) list(spectrum_lay.masses) list(spectrum_lay.probs) for mass, prob in spectrum_lay: print(mass, prob)

new thing: pure generator - only iteration, no storage, for now peak

threshold for mz, prob in iso.IsoThresholdGenerator(formula="C254H377N65O75S6", threshold=minimal_peak_height): print(mz, prob)

My collaborator also told me, that on github under branch version_2_1 there are more examples in the repo, but I guess the above code will be enough.

Sorry for problems: we will add docs in February and make it all more user-friendly. Now, it is much faster than what was in the original version published in Analytical Chemistry though :)

Best wishes,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Mon, Jan 27, 2020 at 7:41 PM Lars Yunker notifications@github.com wrote:

Hi folks, I had been using IsoSpecPy in my python mass spec project and haven't run the test in a little while. It looks like you've changed the imports without including documentation on how I should update my code to support your new structure. I see that in IsoSpecPyOld you discourage users from importing from that module, but it's unclear to me which functions I should be importing instead since the package structure has changed so significantly.

Currently my code is structured like so:

import numpy as np from IsoSpecPy.IsoSpecPy import IsoSpec

iso_spec = IsoSpec.IsoFromFormula( molecular_formula, cutoff=user_threshold_value, ) configurations = iso_spec.getConfs() masses = configurations[0] abundances = [np.exp(val) for val in configurations[1]] ... do other things with the masses and abundances

Since there are no docstrings for classes in the new IsoSpecPy module, it's unclear how I would accomplish this workflow with the new package structure. Could you please provide some guidance as to which things I should be importing or how I should be changing my code?

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[larsyunker]

Hi Matteo, thank you for the prompt response. I have updated my code based on your examples. I like the new generator, but can't utilize it at this time due to some constraints of my code. Unfortunately I need the minimum and maximum mass in the spectrum before beginning iteration, but I will see if I can refactor my code to utilize the generator.

[MatteoLacki]

We are investigating if minimal and maximal masses cannot be calculated for a given joint probability. To get some estimate, you can use the Chebyshev Inequality. This result will always give you an interval that contains the optimal P-set. To make it smaller, you can max the left edge with the lightiest isotopologue that is trivial to calculate.

Best,

On Mon, 27 Jan 2020 at 23:21, Lars Yunker notifications@github.com wrote:

Hi Matteo, thank you for the prompt response. I have updated my code based on your examples. I like the new generator, but can't utilize it at this time due to some constraints of my code. Unfortunately I need the minimum and maximum mass in the spectrum before beginning iteration, but I will see if I can refactor my code to utilize the generator.

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-- Mateusz Krzysztof Łącki

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[larsyunker]

Thank you for the suggestion, I will look into this. I will also keep an eye on your repository in case you implement it before I do.

Cheers

[MatteoLacki]

I had it implemented once, so that is not a bad idea :)

On Mon, 27 Jan 2020 at 23:36, Lars Yunker notifications@github.com wrote:

Thank you for the suggestion, I will look into this. I will also keep an eye on your repository in case you implement it before I do.

Cheers

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-- Mateusz Krzysztof Łącki

​German tel. +49 159 01681376​ Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki