serenipy 0.4.0

Python library for parsing IP2 proteomics file formats (MS2, SQT, DTASelect-filter, Census)

SereniPy

A Python library for parsing and serializing mass spectrometry file formats used in IP2 proteomics pipelines.

Installation

pip install serenipy

Quick Start

MS2 Files

from serenipy import from_ms2, to_ms2

with open("sample.ms2", "r") as f:
    header, spectra = from_ms2(f)

for s in spectra:
    print(s.low_scan, s.mz, s.charge, len(s.mz_spectra))

# Write back to MS2 format
ms2_string = to_ms2(header, spectra)

SQT Files

from serenipy import from_sqt, to_sqt

with open("results.sqt", "r") as f:
    version, header, s_lines = from_sqt(f)

for s_line in s_lines:
    for m_line in s_line.m_lines:
        print(m_line.xcorr, m_line.sequence)

# Write back to SQT format
sqt_string = to_sqt(version, header, s_lines)

DTASelect-filter Files

from serenipy import from_dta_select_filter, to_dta_select_filter

with open("DTASelect-filter.txt", "r") as f:
    version, head, results, tail = from_dta_select_filter(f)

for result in results:
    for protein in result.protein_lines:
        print(protein.locus_name, protein.sequence_coverage)
    for peptide in result.peptide_lines:
        print(peptide.sequence, peptide.x_corr, peptide.charge)

# Write back to DTASelect-filter format
output = to_dta_select_filter(version, head, results, tail)

Census Files

from serenipy import from_census

with open("census.txt", "r") as f:
    header, census_lines = from_census(f)

for line in census_lines:
    print(line.protein, line.pvalue, len(line.experiment_lines))

Supported Formats

Format	Versions	Parse	Serialize
MS2	Standard	from_ms2()	to_ms2()
SQT	V1.4.0, V2.1.0, V2.1.0_ext, V2.1.0_robin_random	from_sqt()	to_sqt()
DTASelect-filter	V2.1.12, V2.1.12_rt, V2.1.12_paser, V2.1.13, V2.1.13_timscore	from_dta_select_filter()	to_dta_select_filter()
Census	Standard	from_census()	-
Census (label-free)	Standard	from_censuslf()	-

All parsers accept either a file-like object or a string as input. Format versions are auto-detected during parsing.

Development

git clone https://github.com/pgarrett-scripps/serenipy.git
cd serenipy
pip install -e ".[dev]"
pytest tests -v

License

MIT