Update mztab output details (#47)

* Update ANN-SoLo CV to the new one in the PSI-MS-CV

* Update the mzTab output mapping

Author: issararab

src/ann_solo/writer.py

@@ -74,7 +74,7 @@ def write_mztab(identifications: List[SpectrumSpectrumMatch], filename: str,
                         f'"{os.path.split(config.query_filename)[1]}" against '
                         f'spectral library file '
                         f'"{os.path.split(config.spectral_library_filename)[1]}"'),
-        ('software[1]', f'[MS, MS:1001456, ANN-SoLo, {__version__}]'),
+        ('software[1]', f'[MS, MS:1003357, ANN-SoLo, {__version__}]'),
         ('psm_search_engine_score[1]', '[MS, MS:1001143, search engine '
                                        'specific score for PSMs,]'),
         ('psm_search_engine_score[2]', '[MS, MS:1002354, PSM-level q-value,]'),
@@ -115,26 +115,39 @@ def write_mztab(identifications: List[SpectrumSpectrumMatch], filename: str,
 
         # SSMs.
         f_out.write('\t'.join([
-            'PSH', 'sequence', 'PSM_ID', 'accession', 'unique', 'database',
-            'database_version', 'search_engine', 'search_engine_score[1]',
-            'search_engine_score[2]', 'modifications', 'retention_time',
-            'charge', 'exp_mass_to_charge', 'calc_mass_to_charge',
-            'spectra_ref', 'pre', 'post', 'start', 'end',
-            'opt_ms_run[1]_cv_MS:1003062_spectrum_index',
-            'opt_ms_run[1]_cv_MS:1002217_decoy_peptide',
-            'opt_ms_run[1]_num_candidates']) + '\n')
+            'PSH',
+            'sequence',
+            'PSM_ID',
+            'accession',
+            'unique',
+            'database',
+            'database_version',
+            'search_engine',
+            'search_engine_score[1]',
+            'search_engine_score[2]',
+            'modifications',
+            'retention_time',
+            'charge',
+            'exp_mass_to_charge',
+            'calc_mass_to_charge',
+            'spectra_ref',
+            'pre',
+            'post',
+            'start',
+            'end',
+            'opt_ms_run[1]_cv_MS:1002217_decoy_peptide']) + '\n')
         # SSMs sorted by their query identifier.
         for ssm in sorted(identifications,
                           key=lambda s: natural_sort_key(s.query_identifier)):
             f_out.write('\t'.join([
                 'PSM',
                 ssm.sequence,
                 str(ssm.query_identifier),
-                'null', 'null',
-                pathlib.Path(os.path.abspath(
-                    config.spectral_library_filename)).as_uri(),
-                database_version,
-                '[MS, MS:1001456, ANN SoLo,]',
+                str(ssm.library_identifier),
+                'null',
+                pathlib.Path(os.path.abspath(config.spectral_library_filename)).as_uri(),
+                lib_reader.get_version(),
+                '[MS, MS:1003357, ANN SoLo,]',
                 str(ssm.search_engine_score),
                 str(ssm.q),
                 'null',
@@ -143,8 +156,10 @@ def write_mztab(identifications: List[SpectrumSpectrumMatch], filename: str,
                 str(ssm.exp_mass_to_charge),
                 str(ssm.calc_mass_to_charge),
                 f'ms_run[1]:index={ssm.query_index}',
-                'null', 'null', 'null', 'null',
-                str(ssm.library_identifier),
+                'null',
+                'null',
+                'null',
+                'null',
                 f'{ssm.is_decoy:d}']) + '\n')
 
     return filename