Writers and controlled vocabulary manager for PSI-MS's mzML and mzIdentML standards
Project description
psims
Prototype work for a unified API for writing PSIMS standardized XML documents, currently just mzML and MzIdentML
See the Documenation for more information
mzML Minimal Example
from psims.mzml.writer import MzMLWriter
# Load the data to write
scans = get_scan_data()
with MzMLWriter(open("out.mzML", 'wb')) as out:
# Add default controlled vocabularies
out.controlled_vocabularies()
# Open the run and spectrum list sections
with out.run(id="my_analysis"):
spectrum_count = len(scans) + sum([len(products) for _, products in scans])
with out.spectrum_list(count=spectrum_count):
for scan, products in scans:
# Write Precursor scan
out.write_spectrum(
scan.mz_array, scan.intensity_array,
id=scan.id, params=[
"MS1 Spectrum",
{"ms level": 1},
{"total ion current": sum(scan.intensity_array)}
])
# Write MSn scans
for prod in products:
out.write_spectrum(
prod.mz_array, prod.intensity_array,
id=prod.id, params=[
"MSn Spectrum",
{"ms level": 2},
{"total ion current": sum(prod.intensity_array)}
],
# Include precursor information
precursor_information={
"mz": prod.precursor_mz,
"intensity": prod.precursor_intensity,
"charge": prod.precursor_charge,
"scan_id": prod.precursor_scan_id
})
Citing
If you use psims
in an academic project, please cite:
Klein, J. A., & Zaia, J. (2018). psims - A declarative writer for mzML and mzIdentML for Python. Molecular & Cellular Proteomics, mcp.RP118.001070. https://doi.org/10.1074/mcp.RP118.001070
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
psims-0.1.29.tar.gz
(5.9 MB
view hashes)
Built Distribution
Close
Hashes for psims-0.1.29-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a7302017d9d1a6cef6b458dca771ec4af50308f25b5ece2c914a0f6b255aaad2 |
|
MD5 | b3c5c90a46e4bcfdcfa328b9533e73ce |
|
BLAKE2b-256 | da19f7383afda5580731a3aa78683204b798893b2628da9db815bbd0e2a454aa |