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Implement explicit matchms remove spectra tool #507

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hechth opened this issue Mar 21, 2024 · 1 comment · Fixed by #517
Closed

Implement explicit matchms remove spectra tool #507

hechth opened this issue Mar 21, 2024 · 1 comment · Fixed by #517
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@hechth
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hechth commented Mar 21, 2024

Since the matchms filtering tool got quite cluttered it would be nice to move the require filters to a dedicated tool.

This tool should have one multiselect as main input where the individual metadata fields are chosen and where spectra which don't have this metadata information are removed.

The options that should be supported are

  • SMILES
  • InChI
  • InChIKey
  • Formula
  • Retention time
  • Retention index
  • Precursor mz
  • Valid Annotation
  • Compound Name

A second input could be a boolean that can output optionally the spectra that have been removed. Another option would be to output a logfile using a identifier (compound_name preferably) or an index if this is not present and to explain because of which missing metadata entry this was removed.

If some of the filters are not available in matchms, they should be added.

The Valid Annotation option should get a help text explaining the functionality as it is implemented in matchms.

@hechth hechth changed the title Update matchms filtering module Implement explicit matchms remove spectra tool Mar 21, 2024
@zargham-ahmad zargham-ahmad self-assigned this Apr 8, 2024
@zargham-ahmad
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for the below filter PR matchms/matchms#627 matchms/matchms#602

  • Formula
  • Retention time
  • Retention index
  • Compound Name

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