enable spectra_ref in mzTab #240
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@WangHong007 the |
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got it @ypriverol |
jpfeuffer
requested changes
Nov 3, 2022
bin/mzml_statistics.py
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| @@ -20,17 +21,19 @@ def parse_mzml(file_name, file_columns): | |||
| name = os.path.split(file_name)[1] | |||
| id = i.getNativeID() | |||
| MSLevel = i.getMSLevel() | |||
| rt = i.getRT() if i.getRT() else np.nan | |||
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* speed up the code. Use less appends, less for loops, less string data
This is about mzml_statistics.py or diann_convert.py?
* write one file per mzml or even per mzml+level
Will do.
What about MS3 ?
Does MS3 have the same attributes as MS2? If so, it can be included in the statement block of MS2 when determining the MSLevel.
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The first comment was about the reading of mzml_info in pmultiqc.
You will usually only have MS3 in TMT. It is similar to MS2 but often has multiple precursors. Not sure if there are important QC metrics on them. We can do it later.
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Now we only count the spectrum id and retention time of MS3 (same as MS1). It will also be recorded in the corresponding *_mzml_info.tsv
bin/mzml_statistics.py
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| def mzml_dataframe(mzml_folder): | ||
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| file_columns = ["File_Name", "SpectrumID", "MSLevel", "Charge", "MS2_peaks", "Base_Peak_Intensity"] | ||
| file_columns = ["File_Name", "SpectrumID", "MSLevel", "Charge", "MS2_peaks", "Base_Peak_Intensity", "Retention_Time", "Exp_Mass_To_Charge"] |
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Not sure if that works without an update in pmultiqc.
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Comments are basically addressed but I think pmultiqc needs to be updated now to make the tests pass? |
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#241 I guess is better I close my PR @WangHong007 and you update yours. I did the changes in your branch @WangHong007 . |
0.0.16 -> 0.0.17
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@ypriverol got it. |
ypriverol
approved these changes
Nov 8, 2022
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