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View Code? Open in Web Editor NEWBuild a local SQLite Database from Massbank.
License: GNU General Public License v3.0
Build a local SQLite Database from Massbank.
License: GNU General Public License v3.0
It might sometimes be useful to build the MassBank database only with retention time (RT) or simply ignoring that some records do not have an MS2.
That needs to be tested.
Iterating over a dataset currently returns a list of spectra per iteration, if the option to group the spectra is set to True. The list of spectra can correspond to, e.g., multiple collision energies.
We should add an option to return merged spectra, as those are required by some downstream functions like MetFrag.
Options to add merging:
Implement a record filter based on the (estimated) column-dead-time to filter out early eluting / non-retaining molecules.
Questions here:
See title. We need a function that can output the MBSpectrum (class) as input text-file for MetFrag or CSI:FingerID.
Check what happens if skip the PubChem update step.
When multiple accessions (spectra / MassBank records) are merged, we need to generate a new accession title and give it as property of the returned MBSpectrum
object.
We can use the procedure from _to_metfrag_output
:
ds = re.compile("[A-Z]+").match(self.get("accession")[0])[0]
_base_fn = ds + sha1("".join(self.get("accession")).encode('utf-8')).hexdigest()[:(8 - len(ds))]
# e.g. AU3a1fd8
The following parameters should be moved to the dataset insertion function:
only_with_rt=True
only_ms2=True
use_pubchem_structure_info=True
exclude_deprecated=True
min_number_of_unique_compounds_per_dataset=50
pc_dbfn=None
Those are only relevant, when data is inserted. Furthermore, the MassbankDB class only acts as a wrapper around the SQLite DB file. It provides standardized functionality to access the data in the DB. It, however, does not (need to) store information about the state of the SQLite DB.
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