Comments (7)
larsyunker
commented on August 19, 2024
Hi Jerry,
I will look into this tomorrow. Would it be possible to share the mzML file in question? With only a brief look at the traceback it seems that the script is looking for a spectrum that isn't present, which is... Curious.
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tanoury1
commented on August 19, 2024
Hi Lars,
I gunzipped the LY....MZml.gz file that was in the validation_files
diretory and used the attached xlms file.
Jerry
…On Tue, Feb 4, 2020 at 7:16 PM Lars Yunker ***@***.***> wrote:
Hi Jerry,
I will look into this tomorrow. Would it be possible to share the mzML
file in question? With only a brief look at the traceback it seems that the
script is looking for a spectrum that isn't present, which is... Curious.
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larsyunker
commented on August 19, 2024
Hi Jerry,
I think I understand now. The xlsx you were trying to use does not match the configuration of the mzML you had targetted (the script was expecting additional functions and modes which are not present in the single-function mzML you had targetted). I have renamed the excel file to hopefully clarify the confusion. I have also added another PySIR example xlsx which pairs with LY-2015-09-15.mzML.gz.
Another feature of the mzML class is reading gzipped files, so you do not need to unzip the mzML file.
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tanoury1
commented on August 19, 2024
Hi Lars,
Thank you so much! It is nice to have all the pieces for a test case so
the user (me) can gain some experience using your code for something that
will work. I'll give it a go asap. I may be getting in touch with you
again once I start using my own data.
Best regards,
Jerry
…On Wed, Feb 5, 2020 at 6:16 PM Lars Yunker ***@***.***> wrote:
Hi Jerry,
I think I understand now. The xlsx you were trying to use does not match
the configuration of the mzML you had targetted (the script was expecting
additional functions and modes which are not present in the single-function
mzML you had targetted). I have renamed the excel file to hopefully clarify
the confusion. I have also added another PySIR example xlsx which pairs
with LY-2015-09-15.mzML.gz.
Another feature of the mzML class is reading gzipped files, so you do not
need to unzip the mzML file.
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tanoury1
commented on August 19, 2024
Hi Lars,
PyRSIR worked. However, even though I had the mzML.gz and .xlsx files
entered in lines 46 and 49, I got a "Directory:" prompt requiring me to
enter the directory that contained the mzML.gz and .xlsx files. I then got
a "Raw or mzML filename:" , "Excel file name:" and "Scans to bin (separate
multiple values with comments):" prompts to add the appropriate
information. For me, that is fine. This allows me to run it from command
line.
I would like to polish the look of the plots that are printed after the run
completes. The title to the Summation plot overlaps with the x-axis of the
Raw Data plot, and there is no legend. Which line belongs to which
species. Where do I find the code that defines the plotting? Or, if you
are able to add that easily?????
Thanks so much for the help,
Jerry
…On Wed, Feb 5, 2020 at 8:43 PM Jerry Tanoury ***@***.***> wrote:
Hi Lars,
Thank you so much! It is nice to have all the pieces for a test case so
the user (me) can gain some experience using your code for something that
will work. I'll give it a go asap. I may be getting in touch with you
again once I start using my own data.
Best regards,
Jerry
On Wed, Feb 5, 2020 at 6:16 PM Lars Yunker ***@***.***>
wrote:
> Hi Jerry,
>
> I think I understand now. The xlsx you were trying to use does not match
> the configuration of the mzML you had targetted (the script was expecting
> additional functions and modes which are not present in the single-function
> mzML you had targetted). I have renamed the excel file to hopefully clarify
> the confusion. I have also added another PySIR example xlsx which pairs
> with LY-2015-09-15.mzML.gz.
>
> Another feature of the mzML class is reading gzipped files, so you do
> not need to unzip the mzML file.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#29?email_source=notifications&email_token=AOA2OYTSXDY6SB7JDHILTMDRBNCFVA5CNFSM4KP7JN2KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEK5KY4Y#issuecomment-582659187>,
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> <https://github.com/notifications/unsubscribe-auth/AOA2OYUXCPPV6X2DZ2YNRALRBNCFVANCNFSM4KP7JN2A>
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larsyunker
commented on August 19, 2024
Hi Jerry,
Sorry the prompting is a legacy thing from how I used to execute scripts. If the script is "run" instead of executed in a Python interpreter the file paths specified in the script are ignored. Command line arguments should be supported, as you've found.
The plots are generated in the plots sub-function of pyrsir (line 95 of the script). You can tweak them as you see fit. It is a matplotlib plot with subplots. I had found that I almost always did extra processing in excel after the fact and usually plotted from that data rather than the raw output of pyrsir. This is why the output plot is so poorly laid out. For naming and interpreting within the pyrsir function, all the data is contained within the sp dictionary. That dictionary is composed of subdictionaries for each key provided in the excel file (the keys of sp are the names defined).
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tanoury1
commented on August 19, 2024
Thank you Lars. The command line approach for pyrsir is fine.
All the best
Jerry
…On Fri, Feb 7, 2020, 5:23 PM Lars Yunker ***@***.***> wrote:
Hi Jerry,
Sorry the prompting is a legacy thing from how I used to execute scripts.
If the script is "run" instead of executed in a Python interpreter the file
paths specified in the script are ignored. Command line arguments should be
supported, as you've found.
The plots are generated in the plots sub-function of pyrsir (line 95 of
the script). You can tweak them as you see fit. It is a matplotlib plot
with subplots. I had found that I almost always did extra processing in
excel after the fact and usually plotted from that data rather than the raw
output of pyrsir. This is why the output plot is so poorly laid out. For
naming and interpreting within the pyrsir function, all the data is
contained within the sp dictionary. That dictionary is composed of
subdictionaries for each key provided in the excel file (the keys of sp
are the names defined).
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