pycompound 0.1.2__tar.gz → 0.1.3__tar.gz

{pycompound-0.1.2/src/pycompound.egg-info → pycompound-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycompound
-Version: 0.1.2
+Version: 0.1.3
 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-0.1.2 → pycompound-0.1.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pycompound"
-version = "0.1.2"
+version = "0.1.3"
 authors = [
   { name="Hunter Dlugas", email="fy7392@wayne.edu" },
 ]

{pycompound-0.1.2 → pycompound-0.1.3}/src/app.py

@@ -884,11 +884,18 @@ def server(input, output, session):
         weights = [float(weight.strip()) for weight in input.weights().split(",") if weight.strip()]
         weights = {'Cosine':weights[0], 'Shannon':weights[1], 'Renyi':weights[2], 'Tsallis':weights[3]}
 
+        high_quality_reference_library_tmp2 = False
+        if input.high_quality_reference_library() != 'False':
+            high_quality_reference_library_tmp2 = True
+
+        print(input.high_quality_reference_library())
+        print(high_quality_reference_library_tmp2)
+
         if input.chromatography_platform() == "HRMS":
-            fig = generate_plots_on_HRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), weights=weights, spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=input.high_quality_reference_library(), mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), window_size_centroiding=input.window_size_centroiding(), window_size_matching=input.window_size_matching(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
+            fig = generate_plots_on_HRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), weights=weights, spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=high_quality_reference_library_tmp2, mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), window_size_centroiding=input.window_size_centroiding(), window_size_matching=input.window_size_matching(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
             plt.show()
         elif input.chromatography_platform() == "NRMS":
-            fig = generate_plots_on_NRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=input.high_quality_reference_library(), mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
+            fig = generate_plots_on_NRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=high_quality_reference_library_tmp2, mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
             plt.show()
         with io.BytesIO() as buf:
             fig.savefig(buf, format="png", dpi=150, bbox_inches="tight")

{pycompound-0.1.2 → pycompound-0.1.3}/src/pycompound/plot_spectra.py

@@ -92,8 +92,8 @@ def generate_plots_on_HRMS_data(query_data=None, reference_data=None, spectrum_I
         print(f'Error: spectrum_preprocessing_order must contain only \'C\', \'F\', \'M\', \'N\', \'L\', \'W\'.')
         sys.exit()
 
-    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','interection','hamming','hellinger']:
-        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, interection, hamming, or hellinger.')
+    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','intersection','hamming','hellinger']:
+        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, intersection, hamming, or hellinger.')
         sys.exit()
 
     if isinstance(int_min,int) is True:
@@ -243,10 +243,12 @@ def generate_plots_on_HRMS_data(query_data=None, reference_data=None, spectrum_I
             r_spec[:,1] = LE_transform(r_spec[:,1], LET_threshold, normalization_method=normalization_method)
         if transformation == 'N' and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
             q_spec = remove_noise(q_spec, nr = noise_threshold)
-            r_spec = remove_noise(r_spec, nr = noise_threshold)
+            if high_quality_reference_library == False or high_quality_reference_library == 'False':
+                r_spec = remove_noise(r_spec, nr = noise_threshold)
         if transformation == 'F' and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
             q_spec = filter_spec_lcms(q_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max, is_matched = is_matched)
-            r_spec = filter_spec_lcms(r_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max, is_matched = is_matched)
+            if high_quality_reference_library == False or high_quality_reference_library == 'False':
+                r_spec = filter_spec_lcms(r_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max, is_matched = is_matched)
 
     q_ints = q_spec[:,1]
     r_ints = r_spec[:,1]
@@ -291,12 +293,15 @@ def generate_plots_on_HRMS_data(query_data=None, reference_data=None, spectrum_I
         plt.yticks([])
 
 
+    print('\n\n\n')
+    print(high_quality_reference_library)
+    print('\n\n\n')
     plt.subplots_adjust(top=0.8, hspace=0.92, bottom=0.3)
     plt.figlegend(loc = 'upper center')
     fig.text(0.05, 0.18, f'Similarity Measure: {similarity_measure.capitalize()}', fontsize=7)
     fig.text(0.05, 0.15, f'Similarity Score: {round(similarity_score,4)}', fontsize=7)
     fig.text(0.05, 0.12, f"Spectrum Preprocessing Order: {''.join(spectrum_preprocessing_order)}", fontsize=7)
-    fig.text(0.05, 0.09, f'High Quality Reference Library: {high_quality_reference_library}', fontsize=7)
+    fig.text(0.05, 0.09, f'High Quality Reference Library: {str(high_quality_reference_library)}', fontsize=7)
     fig.text(0.05, 0.06, f'Window Size (Centroiding): {window_size_centroiding}', fontsize=7)
     fig.text(0.05, 0.03, f'Window Size (Matching): {window_size_matching}', fontsize=7)
     fig.text(0.45, 0.18, f'Raw-Scale M/Z Range: [{mz_min_tmp},{mz_max_tmp}]', fontsize=7)
@@ -387,8 +392,8 @@ def generate_plots_on_NRMS_data(query_data=None, reference_data=None, spectrum_I
         print(f'Error: spectrum_preprocessing_order must contain only \'F\', \'N\', \'W\', \'L\'.')
         sys.exit()
 
-    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','interection','hamming','hellinger']:
-        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, interection, hamming, or hellinger.')
+    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','intersection','hamming','hellinger']:
+        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, intersection, hamming, or hellinger.')
         sys.exit()
 
     if isinstance(int_min,int) is True:
@@ -528,11 +533,11 @@ def generate_plots_on_NRMS_data(query_data=None, reference_data=None, spectrum_I
             r_spec[:,1] = LE_transform(r_spec[:,1], LET_threshold, normalization_method)
         if transformation == 'N':
             q_spec = remove_noise(q_spec, nr = noise_threshold)
-            if high_quality_reference_library == False:
+            if high_quality_reference_library == False or high_quality_reference_library == 'False':
                 r_spec = remove_noise(r_spec, nr = noise_threshold)
         if transformation == 'F':
             q_spec = filter_spec_gcms(q_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max)
-            if high_quality_reference_library == False:
+            if high_quality_reference_library == False or high_quality_reference_library == 'False':
                 r_spec = filter_spec_gcms(r_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max)
 
     if q_spec.shape[0] > 1:
@@ -580,7 +585,7 @@ def generate_plots_on_NRMS_data(query_data=None, reference_data=None, spectrum_I
     fig.text(0.05, 0.15, f'Similarity Measure: {similarity_measure.capitalize()}', fontsize=7)
     fig.text(0.05, 0.12, f'Similarity Score: {round(similarity_score,4)}', fontsize=7)
     fig.text(0.05, 0.09, f"Spectrum Preprocessing Order: {''.join(spectrum_preprocessing_order)}", fontsize=7)
-    fig.text(0.05, 0.06, f'High Quality Reference Library: {high_quality_reference_library}', fontsize=7)
+    fig.text(0.05, 0.06, f'High Quality Reference Library: {str(high_quality_reference_library)}', fontsize=7)
     fig.text(0.05, 0.03, f'Raw-Scale M/Z Range: [{min_mz},{max_mz}]', fontsize=7)
     fig.text(0.45, 0.15, f'Raw-Scale Intensity Range: [{int_min_tmp},{int_max_tmp}]', fontsize=7)
     fig.text(0.45, 0.12, f'Noise Threshold: {noise_threshold}', fontsize=7)

{pycompound-0.1.2 → pycompound-0.1.3/src/pycompound.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycompound
-Version: 0.1.2
+Version: 0.1.3
 Summary: Python package to perform compound identification in mass spectrometry via spectral library matching.
 Author-email: Hunter Dlugas <fy7392@wayne.edu>
 License-Expression: MIT