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Add unispec to Koina #98

Merged
merged 21 commits into from
Jul 31, 2024
Merged

Add unispec to Koina #98

merged 21 commits into from
Jul 31, 2024

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LLautenbacher
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jlapin1 and others added 12 commits July 2, 2024 12:04
@jlapin1 @LLautenbacher
Rebase unispec branch to main
267aa90
@jlapin1 @LLautenbacher
Working code from labels to 7919 output. Renamed uspreprocess to
8036aa1 
usprocess
@jlapin1 @LLautenbacher
Still working code from labels to 7919 intensity spectra. Saving state
ca129bd 
of model before I begin editing input to accomodate more Wilhelm lab-friendly input structures.
@jlapin1 @LLautenbacher
Working code to output full 7919 intensities with mz and annotation.
2355b9c 
Note
- both mz and intensities had residuals as high as <5e-4
- annotations are still in model's internal notation
@jlapin1 @LLautenbacher
Working model that outputs 200 top peaks by intensity. Also applies a
b7e9827 
filter that sets intensity to -1 for every impossible prediction.
@jlapin1 @LLautenbacher
model.pt is replaced with .zenodo file pointing to model link on
266cd4e 
zenodo. Also added a notes.yaml file for documentation.
@jlapin1 @LLautenbacher
Updated internal notation to Int/{seq}/{start}
7e94720 
Fixed bug regarding string comparisons in filter_fake
@jlapin1 @LLautenbacher
Updated allowed instrument types
476ae2a
@jlapin1 @LLautenbacher
Added NONE as acceptable instrument type to NCE2eV function.
96c308f
@jlapin1 @LLautenbacher
Updated the notes.yaml in usprocess folder of Unispec
03f2011
@jlapin1 @LLautenbacher
Updated test to load charges energies and sequences instead of labels.
95b0bb5
@LLautenbacher
Apply formatting
abfaa00
@LLautenbacher LLautenbacher added the patch Used for automatic semantic versioning of releases. label Jul 2, 2024
LLautenbacher
LLautenbacher commented Jul 5, 2024
View reviewed changes
clients/python/test/UniSpec/labels_input.txt Outdated Show resolved Hide resolved
clients/python/test/UniSpec/labels_input2.txt Outdated Show resolved Hide resolved
clients/python/test/UniSpec/old/script.py Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_unispec23.py Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_usprocess.py Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_output_mz2.npy Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_output_top200_int2.npy Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_output_top200_ions2.npy Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_output_top200_mz2.npy Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_unispec23.py Show resolved Hide resolved
LLautenbacher
LLautenbacher commented Jul 26, 2024
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clients/python/test/UniSpec/test_UniSpec_usprocess.py Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_unispec23.py Outdated Show resolved Hide resolved
clients/python/test/UniSpec/test_usprocess.py Outdated Show resolved Hide resolved
@LLautenbacher LLautenbacher merged commit b537c2e into main Jul 31, 2024
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@LLautenbacher @jlapin1