psims 0.1.26

Writers and controlled vocabulary manager for PSI-MS's mzML and mzIdentML standards

# psims
Prototype work for a unified API for writing PSIMS standardized XML documents, currently just mzML and MzIdentML

See the [Documenation](https://mobiusklein.github.io/psims) for more information

## mzML Minimal Example

```python
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
})
```