Functional .msp output

compomics · May 7, 2024 · c6073e1 · c6073e1
1 parent 4cf2fde
commit c6073e1
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Showing 4 changed files with 164 additions and 116 deletions.
diff --git a/ms2pip/__main__.py b/ms2pip/__main__.py
@@ -20,7 +20,7 @@
     UnresolvableModificationError,
 )
 from ms2pip.result import correlations_to_csv, results_to_csv
-from ms2pip.spectrum_output import write_single_spectrum_csv, write_single_spectrum_png
+from ms2pip.spectrum_output import write_single_spectrum_csv, write_single_spectrum_png, SpectrumOutput
 
 console = Console()
 logger = logging.getLogger(__name__)
@@ -125,6 +125,10 @@ def predict_library(*args, **kwargs):
     logger.info(f'Writing output to {output_name_csv}')
     results_to_csv(predictions, output_name_csv)
     logger.info(f'Finished writing output to {output_name_csv}')
+    #TODO: add support for other output formats
+    # Initial implementation of writing to MSP format
+    so = SpectrumOutput(predictions, normalization="basepeak_10000")
+    so.write_msp()
 
 
 

diff --git a/ms2pip/result.py b/ms2pip/result.py
@@ -138,7 +138,7 @@ def results_to_csv(results: List["ProcessingResult"], output_file: str) -> None:
                         writer.writerow(
                             {
                                 "psm_index": result.psm_index,
-                                "peptidoform": result.psm.peptidoform,
+                                "peptidoform": result.psm.peptidoform, #TODO Remove this, was for checking correctness
                                 "ion_type": ion_type,
                                 "ion_number": i + 1,
                                 "mz": "{:.6g}".format(result.theoretical_mz[ion_type][i]),

diff --git a/ms2pip/search_space.py b/ms2pip/search_space.py
@@ -69,7 +69,7 @@ def into_psm_list(self, min_precursor_mz = 0, max_precursor_mz = np.Inf) -> PSML
         for modifications, charge in product(self.modification_options, self.charge_options):
             offset = 0
             if not modifications:
-                psm = PSM(peptidoform=(self.sequence+'/{}'.format(charge)), spectrum_id=spectrum_id)
+                psm = PSM(peptidoform=(self.sequence+'/{}'.format(charge)), spectrum_id=spectrum_id, protein_list=self.proteins)
                 spectrum_id += 1
             else:
                 modded_sequence = list(self.sequence)
@@ -86,7 +86,7 @@ def into_psm_list(self, min_precursor_mz = 0, max_precursor_mz = np.Inf) -> PSML
                         modded_sequence.append(f"-[{mod}]")
 
                 modded_sequence = "".join(modded_sequence)
-                psm = PSM(peptidoform=(modded_sequence+'/{}'.format(charge)), spectrum_id=spectrum_id)
+                psm = PSM(peptidoform=(modded_sequence+'/{}'.format(charge)), spectrum_id=spectrum_id, protein_list=self.proteins)
                 spectrum_id += 1
             if psm.peptidoform.theoretical_mz >= min_precursor_mz and psm.peptidoform.theoretical_mz <= max_precursor_mz:
                 psms.append(psm)