hunter-moseley
commented
1 year ago Look at fileio.py submodule to understand how to use MWTabFile objects. https://github.com/MoseleyBioinformaticsLab/mwtab/blob/master/mwtab/fileio.py
The MWTabFile init takes a filename, but the read method is used to read from a filehandle. It is a little messy, but it was designed to capture the source whether it was a filename, a URL, or a filepath in a zip archive.
Could use the tempfile module to create a temporary JSON file to read in. https://docs.python.org/3/library/tempfile.html Then could use: mwtabfile = mwtab.MWTabFile(filename-to-save-to) mwtabfile.read(tempfile_handle)
On Thu, Nov 3, 2022 at 9:22 AM ptth222 @.***> wrote:
The whole package essentially assumes everything is starting from a file on disk, so if you already have a JSON dictionary constructed in memory it is not straightforward to create the mwTab format file. One method is to save the JSON out and then read it back in.
Excerpt from old MESSES convert code:
mwtab_json_fpath = "{}.json".format(splitext(results_path)[0]) mwtab_txt_fpath = "{}.txt".format(splitext(results_path)[0])
save JSON
with open(mwtab_json_fpath, 'w', encoding="utf-8") as outfile: json.dump(mwtabfile, outfile, indent=4)
save mwTab (.txt)
with open(mwtab_txt_fpath, 'w', encoding="utf-8") as outfile: mwfile = next(mwtab.read_files(mwtab_json_fpath)) mwfile.write(outfile, file_format="mwtab")
Another way is a bit hacky:
mwtabfile = mwtab.mwtab.MWTabFile("") mwtabfile.update(output_json) mwtabfile.header = " ".join( ["#METABOLOMICS WORKBENCH"]
- [item[0] + ":" + item[1] for item in mwtabfile["METABOLOMICS WORKBENCH"].items() if item[0] not in ["VERSION", "CREATED_ON"]] ) with open(args["
"], 'w', encoding='utf-8') as outfile: mwtabfile.write(outfile, file_format="mwtab") The MWTabFile class has a strange init. It requires a "source" input that is supposed to be the path to the file I think, but then self.source is never used by any of its methods. Similarly self.study_id and self.analysis_id are set in the read method and not used. self.header is also set in the read method and then used in the print_file method rather than just printing the header when it is needed like every other section. I feel like this should be retooled so it can accept an initial JSON in the init, and maybe clean up some of the unused stuff, but I don't know that they aren't used in other parts of the package.
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-- Hunter Moseley, Ph.D. -- Univ. of Kentucky Professor, Dept. of Molec. & Cell. Biochemistry / Markey Cancer Center / Institute for Biomedical Informatics / UK Superfund Research Center Not just a scientist, but a fencer as well. My foil is sharp, but my mind sharper still.
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ptth222
The whole package essentially assumes everything is starting from a file on disk, so if you already have a JSON dictionary constructed in memory it is not straightforward to create the mwTab format file. One method is to save the JSON out and then read it back in.
Excerpt from old MESSES convert code:
Another way is a bit hacky:
The MWTabFile class has a strange init. It requires a "source" input that is supposed to be the path to the file I think, but then self.source is never used by any of its methods. Similarly self.study_id and self.analysis_id are set in the read method and not used. self.header is also set in the read method and then used in the print_file method rather than just printing the header when it is needed like every other section. I feel like this should be retooled so it can accept an initial JSON in the init, and maybe clean up some of the unused stuff, but I don't know that they aren't used in other parts of the package.