mztabpy
Python library to handle mztab files. mzTab is a tab-delimited file format created by HUPO-PSI containing protein/peptide quantification and identification data.
Input
mztab_convert
mzTab
hdf5_search
HDF5
Output
mztab_convert
Metadata, protein, peptide, and PSM subtables(.csv) or HDF5 file(.hdf5) with the four parts of information.
hdf5_search
A dataframe that can be filtered or already filtered based on the condition.
Usage
mztab_convert
python mztabpy_click.py mztab_convert --mztab_path {mztab_path} --directory {result folder} --type {result type} --section {section of the mzTab} --removemeta {True or False}
hdf5_search
python mztabpy_click.py hdf5_search --hdf5_path {hdf5_path} --subtable {section of the mzTab} --where {filtering condition}
Parameters
mztab_convert
- --mztab_path: The path to mzTab
- --directory: Folder to result files. Default "./"
- --type: Result type(
"tsv","hdf5"or"all"). Default "all" - --section: Indicates the data section of the mzTab that is required.
"all","protein","peptide"or"psm".Default "all" - --removemeta: Whether to remove
metadata. Default False
hdf5_search
- --hdf5_path: Path to HDF5
- --section: Indicates the data section of the mzTab that is required.
"protein","peptide"or"psm". - --where: The filtering condition of the corresponding chunk is expressed as the key-value pair in one string, e.g.
"accession:P45464,sequence:TIQQGFEAAK", default None
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