OpenMSUtils

This open source project is used for easily reading and processing MS files and Fasta files.

Usage

first, install the package, you can use pip to install the package

pip install git+https://github.com/Elcherneske/OpenMSUtils.git

or

git clone https://github.com/Elcherneske/OpenMSUtils.git
cd OpenMSUtils
pip install .

Read MS file

This package provides various classes for reading MS files, including MZML, MGF, MS1, and MS2.

Here is a detailed example of reading an MS file using MZMLReader and converting the spectra to MSObject using SpectraConverter:

from OpenMSUtils.SpectraUtils import MZMLReader, SpectraConverter

# Step 1: Initialize the MZMLReader
reader = MZMLReader()

# Step 2: Specify the path to your mzML file
file_path = "path/to/your/test.mzML"

# Step 3: Read the mzML file
# You can choose to parse spectra in parallel for better performance
mzml_obj = reader.read(file_path, parse_spectra=True, parallel=True)

# Step 4: Access the spectra from the MZMLObject
if mzml_obj.run and mzml_obj.run.spectra_list:
    print(f"成功读取 {len(mzml_obj.run.spectra_list)} 个谱图")

    # Step 5: Iterate through the spectra and convert them to MSObject
    ms_objects = []
    for spectrum in mzml_obj.run.spectra_list:
        ms_obj = SpectraConverter.to_msobject(spectrum)
        ms_objects.append(ms_obj)
    print(f"转换成功: {spectrum.attrib.get('id', 'N/A')} -> MSObject")

    # Step 6: Access properties of the MSObject
    for ms_obj in ms_objects:
    print(f"MS级别: {ms_obj.level}")
    print(f"保留时间: {ms_obj.retention_time:.2f}秒")
    print(f"峰值数量: {len(ms_obj.peaks)}")
else:
    print("未读取到谱图数据")

Here is an example of using MSObject

from OpenMSUtils.SpectraUtils import MSObject, SpectraConverter

ms_object = SpectraConverter.to_msobject(spectrum)

# get peaks from ms_object
peaks = ms_object.peaks

# get precursor from ms_object
precursor = ms_object.precursor

# get scan_info from ms_object
scan_info = ms_object.scan

# get ms level from ms_object
ms_level = ms_object.level

# get additional_info from ms_object
additional_info = ms_object.additional_info

# get scan_number from ms_object
scan_number = ms_object.scan_number

# get retention_time from ms_object
retention_time = ms_object.retention_time

Here is an example of reading MS file from mgf, ms1, ms2:

from OpenMSUtils.SpectraUtils import MZMLReader, MGFReader, MS1Reader, MS2Reader

reader = MGFReader()
meta_data, spectrum = reader.read(file_path)

reader = MS1Reader()
meta_data, spectrum = reader.read(file_path)

reader = MS2Reader()
meta_data, spectrum = reader.read(file_path)

ion mobility spectrum

this package provides various classes for reading and processing ion mobility spectrum

Here is an example of reading ion mobility spectrum:

from OpenMSUtils.SpectraUtils import MZMLReader, SpectrumPlotter, IonMobilityUtils

reader = MZMLReader()
meta_data, spectra = reader.read(file_path)

ion_mobility_utils = IonMobilityUtils()
ion_mobility_utils.get_ion_mobility(spectra[start_index:end_index])

plotter = SpectrumPlotter()
plotter.plot_ion_mobility(ion_mobility_utils.ion_mobility_spectrum, time_range=(0, 100), mz_range=(0, 1000), time_bins=200, mz_bins=200)

Read Fasta file && Write Fasta file

from OpenMSUtils.FastaUtils import FastaReader, FastaWriter

reader = FastaReader()
sequences = reader.read(file_path)

#sequences: {head: sequence, ...}
writer = FastaWriter()
writer.write(sequences, file_path)

Nucleic Acid

This package provides various classes for processing nucleic acid sequences, including oligonucleotide sequences, DNA sequences, and RNA sequences.

Here is an example of processing nucleic acid sequences:

from OpenMSUtils.MolecularUtils import NucleicAcidUtils

# generate a oligonucleotide sequence
sequence = NucleicAcidUtils.Oligonucleotide("ATCG")

# add modifications to the sequence
sequence.add_modification(0, NucleicAcidUtils.Modification("Phosphorylation", "HPO3"))

# add end modifications to the sequence
sequence.add_end_modifications(("Phosphorylation", "HPO3"), ("Phosphorylation", "HPO3"))

# set charge of the sequence
sequence.set_charge(1)

# set adduct of the sequence
sequence.set_adduct("H+")

# generate fragments of oligonucleotide
fragments = sequence.fragments

# get the mass of the sequence
mass = sequence.mass