Gzip flag overrides output file flag

[lazear]

Hi,

Using a combination of -g and -b flags produces an unexpected result.

.\ThermoRawFileParser.exe -N -f 1 -g -i="test.raw" -b="test.mzML.gz" creates a file named "test.mzML.gz.gzip"

I would also like to request, perhaps, that the default extension for using the -g flag be changed to .gz, which is the standard extension from gzipped files (for instance, gunzip doesn't recognize .gzip....)

[caetera]

Hi @lazear,

thank you for reporting this issue. Do I understand correctly, that "less surprising" result will be to use provided filename as it is (in layman terms - "user knows better")?
For example, .\ThermoRawFileParser.exe -g -i="test.raw" -b="test.mzML" should generate test.mzML that is in fact a gzipped one.

[edeutsch]

Sorry to barge in on the convo, but I think the least surprising is if:
.\ThermoRawFileParser.exe -g -i="test.raw" -b="test.mzML"
generates test.mzML.gz

and:
.\ThermoRawFileParser.exe -g -i="test.raw" -b="test.mzML.gz"
generates test.mzML.gz

(like "Save As...." applications with format selection do)

[lazear]

thank you for reporting this issue. Do I understand correctly, that "less surprising" result will be to use provided filename as it is (in layman terms - "user knows better")? For example, .\ThermoRawFileParser.exe -g -i="test.raw" -b="test.mzML" should generate test.mzML that is in fact a gzipped one.

I would expect the generated mzML file name to exactly match the file name passed by the -b file ("user knows better"), but I think @edeutsch's suggestion (where the gz file extension is appended if not present) is probably the better approach for most users/applications (which generally rely on file extensions)

[caetera]

Thank you both for your input. I will stick to "add the extension, if it is not present". I guess, for unification, the same behavior should be added to other file formats, i.e. add .mzML to all mzML files, if it is not present and so on.

[caetera]

I have implemented the changes and added a test with the following table of test cases (with as strange user inputs as I can come with). Please, let me know, if there is any case that I might forgot to include. (I guess the table is rather self-explanatory)

Format	Gzip	UserInput	FileOutput
MGF	FALSE	rawfile	rawfile.mgf
MGF	FALSE	rawfile.	rawfile.mgf
MGF	FALSE	rawfile.mgf	rawfile.mgf
MGF	FALSE	rawfile.MGF	rawfile.mgf
MGF	FALSE	rawfile..	rawfile.mgf
MGF	TRUE	rawfile.mgf.gz	rawfile.mgf.gz
MGF	TRUE	rawfile	rawfile.mgf.gz
MGF	TRUE	rawfile..	rawfile.mgf.gz
MGF	TRUE	rawfile.mgf.GZ	rawfile.mgf.gz
MGF	TRUE	rawfile.mgf	rawfile.mgf.gz
MGF	TRUE	rawfile.MGF.	rawfile.mgf.gz
mzML	FALSE	rawfile	rawfile.mzML
mzML	FALSE	rawfile.	rawfile.mzML
mzML	FALSE	rawfile.mgf	rawfile.mgf.mzML
mzML	FALSE	rawfile.MzML	rawfile.mzML
mzML	FALSE	rawfile..	rawfile.mzML
mzML	TRUE	rawfile.mzML.gz	rawfile.mzML.gz
mzML	TRUE	rawfile	rawfile.mzML.gz
mzML	TRUE	rawfile..	rawfile.mzML.gz
mzML	TRUE	rawfile.mzml.GZ	rawfile.mzML.gz
mzML	TRUE	rawfile.mzML	rawfile.mzML.gz
mzML	TRUE	rawfile.MZml.	rawfile.mzML.gz

[lazear]

That looks good to me, thank you for tackling this @caetera! I think it would also be good to update the documentation & CLI flag help to clarify that the flag only effects the filename, and not the full file path.

[caetera]

Closed in version 1.4.2