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Merged
Jhsmit merged 35 commits into from
Dec 17, 2025
Merged

Update formats #16

Jhsmit merged 35 commits into from
Dec 17, 2025

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@Jhsmit Jhsmit commented Dec 11, 2025 •
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Adds support for HD examiner peptide pool and uptake summary data.

The data format 'HDExaminer_v3' was refactored to 'HDexaminer_all_results'
There was another variant added on HD examiner all results: 'HDExaminer_all_results_with_units'
which has units Da in some of the columns
See FormatSpec docstrings for more details

  • refactor FormatSpecs to be classes instead of instances
  • moved load_peptides function to process
  • aggregation now also outputs number of charged states (n_charges), number of replicates (n_replicates) and total number of isotopic clusters (n_clusters) used in averaging.

Jhsmit added 30 commits December 9, 2025 18:37
@Jhsmit
add reading hd examiner peptide pool
786adb5
@Jhsmit
prepare for identify by path
0d6a223
@Jhsmit
add protein filter field
9a3964c
@Jhsmit
refactor loader to reader, rework formats
448479b
@Jhsmit
remove combined schema
e29079c
@Jhsmit
fix peptide pool reader and add tests
09464ff
@Jhsmit
add kingfisher HD examiner example file
019e24c
@Jhsmit
refactor peptide pool reader
561e230
@Jhsmit
refactor: update format handling and improve peptide loading function…
103810c 
…ality
@Jhsmit
example of only reading files
961d9f7
@Jhsmit
fix loading datasets example
e9f380a
@Jhsmit
add protein field to docs
627f780
@Jhsmit
add hd examiner peptides files
5fa2458
@Jhsmit
cast exposure can also raise ValueError
74eb719
@Jhsmit
group by protein and state such that dataframes can be aggregated in …
6e0749e 
…batch
@Jhsmit
fix hd examiner format identification
95d7895
@Jhsmit
aggregate replicate, cluster and charge count
9461f2a
@Jhsmit
add summary function
c19c43d
@Jhsmit
add uptake summary table
916b973
@Jhsmit
add load method to formats
e362e0f
@Jhsmit
fix format names
72c45e8
@Jhsmit
add uptake summary converter
5ba3ff9
@Jhsmit
renew test data with n_charges column
3adf0fe
@Jhsmit
expand docs on n_charges
f45d70f
@Jhsmit
add function to find offset between structure and peptides
ef846aa
@Jhsmit
update docstring and allow selecting mutiple columns on join
6fac61b
@Jhsmit
make publication title required
4dd0861
@Jhsmit
support loading from .zip files
25e9973
@Jhsmit
allow loading form dir also when there is only 1 dataset present
6e67f95
@Jhsmit
delete comment
37e40c5
@Jhsmit Jhsmit merged commit afb81a3 into master Dec 17, 2025
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@Jhsmit