pycompound 0.1.9__py3-none-any.whl → 0.1.10__py3-none-any.whl

pycompound/plot_spectra.py

@@ -14,7 +14,7 @@ def generate_plots_on_HRMS_data(query_data=None, reference_data=None, spectrum_I
     else:
         extension = query_data.rsplit('.',1)
         extension = extension[(len(extension)-1)]
-        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF':
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
             output_path_tmp = query_data[:-3] + 'txt'
             build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=True)
             df_query = pd.read_csv(output_path_tmp, sep='\t')
@@ -29,7 +29,7 @@ def generate_plots_on_HRMS_data(query_data=None, reference_data=None, spectrum_I
     else:
         extension = reference_data.rsplit('.',1)
         extension = extension[(len(extension)-1)]
-        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF':
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
             output_path_tmp = reference_data[:-3] + 'txt'
             build_library_from_raw_data(input_path=reference_data, output_path=output_path_tmp, is_reference=True)
             df_reference = pd.read_csv(output_path_tmp, sep='\t')
@@ -298,7 +298,7 @@ def generate_plots_on_NRMS_data(query_data=None, reference_data=None, spectrum_I
     else:
         extension = query_data.rsplit('.',1)
         extension = extension[(len(extension)-1)]
-        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF':
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
             output_path_tmp = query_data[:-3] + 'txt'
             build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
             df_query = pd.read_csv(output_path_tmp, sep='\t')
@@ -312,7 +312,7 @@ def generate_plots_on_NRMS_data(query_data=None, reference_data=None, spectrum_I
     else:
         extension = reference_data.rsplit('.',1)
         extension = extension[(len(extension)-1)]
-        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF':
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
             output_path_tmp = reference_data[:-3] + 'txt'
             build_library_from_raw_data(input_path=reference_data, output_path=output_path_tmp, is_reference=True)
             df_reference = pd.read_csv(output_path_tmp, sep='\t')
@@ -395,8 +395,8 @@ def generate_plots_on_NRMS_data(query_data=None, reference_data=None, spectrum_I
         print(f'Warning: plots will be saved to the PDF ./spectrum1_{spectrum_ID1}_spectrum2_{spectrum_ID2}_plot.pdf in the current working directory.')
         output_path = f'{Path.cwd()}/spectrum1_{spectrum_ID1}_spectrum2_{spectrum_ID2}.pdf'
 
-    min_mz = np.min([np.min(df_query['mz_ratio'].tolist()), np.min(df_reference['mz_ratio'].tolist())])
-    max_mz = np.max([np.max(df_query['mz_ratio'].tolist()), np.max(df_reference['mz_ratio'].tolist())])
+    min_mz = int(np.min([np.min(df_query['mz_ratio'].tolist()), np.min(df_reference['mz_ratio'].tolist())]))
+    max_mz = int(np.max([np.max(df_query['mz_ratio'].tolist()), np.max(df_reference['mz_ratio'].tolist())]))
     mzs = np.linspace(min_mz,max_mz,(max_mz-min_mz+1))
 
     unique_query_ids = df_query['id'].unique().tolist()

pycompound/spec_lib_matching.py

@@ -65,7 +65,7 @@ def tune_params_DE(query_data=None, reference_data=None, chromatography_platform
         extension = extension[(len(extension)-1)]
         if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
             output_path_tmp = query_data[:-3] + 'txt'
-            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=True)
             df_query = pd.read_csv(output_path_tmp, sep='\t')
         if extension == 'txt' or extension == 'TXT':
             df_query = pd.read_csv(query_data, sep='\t')
@@ -805,7 +805,7 @@ def run_spec_lib_matching_on_NRMS_data(query_data=None, reference_data=None, lik
     else:
         extension = query_data.rsplit('.',1)
         extension = extension[(len(extension)-1)]
-        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF':
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
             output_path_tmp = query_data[:-3] + 'txt'
             build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
             df_query = pd.read_csv(output_path_tmp, sep='\t')

{pycompound-0.1.9.dist-info → pycompound-0.1.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycompound
-Version: 0.1.9
+Version: 0.1.10
 Summary: Python package to perform compound identification in mass spectrometry via spectral library matching.
 Author-email: Hunter Dlugas <fy7392@wayne.edu>
 License-Expression: MIT

{pycompound-0.1.9.dist-info → pycompound-0.1.10.dist-info}/RECORD

@@ -1,14 +1,14 @@
 pycompound/build_library.py,sha256=4S8hT8FSrS_13daCdsva5UCEU-1qy9pD7kaaG-vaxvE,6815
-pycompound/plot_spectra.py,sha256=Y_onxNnw36LU5JnY_Frywgh6KLEawlfEjy4vfc67MII,32151
+pycompound/plot_spectra.py,sha256=XW_UHgmPCdjsTD5oiNrszuW5GHyfBslcpXM9_bYg66I,32521
 pycompound/plot_spectra_CLI.py,sha256=ObaLad5Z5DmfQB-j0HSCg1mLORbYj2BM3hb5Yd0ZdDI,8395
 pycompound/processing.py,sha256=NsLI994MRlDq7M13LE-1RkfAfgVjHLrLLPbu2SvArKg,10684
 pycompound/similarity_measures.py,sha256=NbeVIy9DE_KWlDMXXylekjKuYVrtzbeEXbTutKFxmfU,10460
-pycompound/spec_lib_matching.py,sha256=T1ymN_KiUTUM8oPeTNOSwdup5Vg8RLEVbzNRZRNOozY,54557
+pycompound/spec_lib_matching.py,sha256=y-4sWt7fphzFKXeURWgosLj8cNIBrcfUOaiCToELvgQ,54646
 pycompound/spec_lib_matching_CLI.py,sha256=L1D1j3MDdIe7th5n47z4uyvR5tL_8lN_22kbc-J7CF8,12053
 pycompound/tuning_CLI_DE.py,sha256=VRxoPLvuvE1gTRMC_lrOOK8TjINinMV_f4q69uDK2oE,9916
 pycompound/tuning_CLI_grid.py,sha256=lavROwKfJSi7xLaUX0zEaphlq7sJ-1FVY3hY3tWwoV4,9735
-pycompound-0.1.9.dist-info/licenses/LICENSE,sha256=fPFFlkSGg60VQWyWqTSv8yoJnpLzppzdihVWY5NKom8,1064
-pycompound-0.1.9.dist-info/METADATA,sha256=gZ1iVV-qOYTXe3HGCjcU-tT950xBWP70Snaf3w9dN0w,1746
-pycompound-0.1.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-pycompound-0.1.9.dist-info/top_level.txt,sha256=x7XjCCdlf335pIEf2TkiFHDrpbSaogk0zg1gPzKe-ic,11
-pycompound-0.1.9.dist-info/RECORD,,
+pycompound-0.1.10.dist-info/licenses/LICENSE,sha256=fPFFlkSGg60VQWyWqTSv8yoJnpLzppzdihVWY5NKom8,1064
+pycompound-0.1.10.dist-info/METADATA,sha256=v1A52MHLSpf1Ty2sMxx-FwdPY7pFIxFvYFWNb86Od4s,1747
+pycompound-0.1.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pycompound-0.1.10.dist-info/top_level.txt,sha256=x7XjCCdlf335pIEf2TkiFHDrpbSaogk0zg1gPzKe-ic,11
+pycompound-0.1.10.dist-info/RECORD,,