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Reimplement predict library #219

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May 8, 2024
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8 changes: 4 additions & 4 deletions .github/workflows/test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -35,11 +35,11 @@ jobs:

- name: Build and install ms2pip
run: |
pip install .[test]
pip install .[dev]

# - name: Test with pytest
# run: |
# pytest
- name: Test with pytest
run: |
pytest

- name: Test installation
run: |
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6 changes: 6 additions & 0 deletions docs/source/api/ms2pip.search-space.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
*******************
ms2pip.search_space
*******************

.. automodule:: ms2pip.search_space
:members:
14 changes: 12 additions & 2 deletions docs/source/usage.rst
Original file line number Diff line number Diff line change
Expand Up @@ -33,12 +33,22 @@ results in:
``predict-batch``
-----------------

[todo]
Provide a list of peptidoforms (see :ref:`Peptides / PSMs`) to predict multiple spectra at once.
For instance,

.. code-block:: sh

ms2pip predict-batch peptides.tsv --model TMT

results in a file ``test_predictions.csv`` with the predicted spectra.


``predict-library``
-------------------

[todo]
Predict spectra for a full peptide search space generated from a protein FASTA file. Various
peptide search space parameters can be configured to control the peptidoforms that are generated.
See :ref:`ms2pip.search_space` for more information.

This mode was first developed in collaboration with the ProGenTomics group for the
`MS²PIP for DIA <https://github.com/brvpuyve/MS2PIP-for-DIA>`_ project.
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Empty file removed fasta2speclib/__init__.py
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