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