pycompound 0.0.7__tar.gz → 0.0.9__tar.gz

{pycompound-0.0.7 → pycompound-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycompound
-Version: 0.0.7
+Version: 0.0.9
 Summary: Python package to perform compound identification in mass spectrometry via spectral library matching.
 Author-email: Hunter Dlugas <fy7392@wayne.edu>
 License-Expression: MIT
@@ -19,6 +19,7 @@ Requires-Dist: pyteomics==4.7.2
 Requires-Dist: netCDF4==1.6.5
 Requires-Dist: lxml>=5.1.0
 Requires-Dist: orjson==3.11.0
+Requires-Dist: shiny==1.4.0
 Requires-Dist: joblib==1.5.2
 Dynamic: license-file
 

{pycompound-0.0.7 → pycompound-0.0.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pycompound"
-version = "0.0.7"
+version = "0.0.9"
 authors = [
   { name="Hunter Dlugas", email="fy7392@wayne.edu" },
 ]
@@ -27,6 +27,7 @@ dependencies = [
     "netCDF4==1.6.5",
     "lxml>=5.1.0",
     "orjson==3.11.0",
+    "shiny==1.4.0",
     "joblib==1.5.2"
 ]
 

{pycompound-0.0.7 → pycompound-0.0.9}/src/app.py

@@ -1,17 +1,20 @@
 
 from shiny import App, ui, reactive, render
-from pycompound_fy7392.spec_lib_matching import run_spec_lib_matching_on_HRMS_data 
-from pycompound_fy7392.spec_lib_matching import run_spec_lib_matching_on_NRMS_data 
-from pycompound_fy7392.spec_lib_matching import tune_params_on_HRMS_data
-from pycompound_fy7392.spec_lib_matching import tune_params_on_NRMS_data
-from pycompound_fy7392.plot_spectra import generate_plots_on_HRMS_data
-from pycompound_fy7392.plot_spectra import generate_plots_on_NRMS_data
+from pycompound.spec_lib_matching import run_spec_lib_matching_on_HRMS_data 
+from pycompound.spec_lib_matching import run_spec_lib_matching_on_NRMS_data 
+from pycompound.spec_lib_matching import tune_params_on_HRMS_data
+from pycompound.spec_lib_matching import tune_params_on_NRMS_data
+from pycompound.plot_spectra import generate_plots_on_HRMS_data
+from pycompound.plot_spectra import generate_plots_on_NRMS_data
 from pathlib import Path
 import subprocess
 import traceback
 import asyncio
 import io
+#import matplotlib
+#matplotlib.use('agg')
 import matplotlib.pyplot as plt
+#from matplotlib.figure import Figure
 
 
 def plot_spectra_ui(platform: str):
@@ -71,7 +74,7 @@ def plot_spectra_ui(platform: str):
     )
 
     # Run and Back buttons
-    run_button = ui.input_action_button("run_btn", "Run", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
+    run_button_plot_spectra = ui.download_button("run_btn_plot_spectra", "Run", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
     back_button = ui.input_action_button("back", "Back to main menu", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
 
     #print(len(extra_inputs))
@@ -98,7 +101,7 @@ def plot_spectra_ui(platform: str):
         ui.TagList(
             ui.h2("Plot Spectra"),
             inputs_columns,
-            run_button,
+            run_button_plot_spectra,
             back_button
         ),
     )
@@ -155,10 +158,9 @@ def run_spec_lib_matching_ui(platform: str):
 
 
     # Run and Back buttons
-    run_button = ui.input_action_button("run_btn", "Run", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
+    run_button_spec_lib_matching = ui.download_button("run_btn_spec_lib_matching", "Run", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
     back_button = ui.input_action_button("back", "Back to main menu", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
 
-    #print(len(extra_inputs))
     # Layout base_inputs and extra_inputs in columns
     if platform == "HRMS":
         inputs_columns = ui.layout_columns(
@@ -182,7 +184,7 @@ def run_spec_lib_matching_ui(platform: str):
         ui.TagList(
             ui.h2("Run Spectral Library Matching"),
             inputs_columns,
-            run_button,
+            run_button_spec_lib_matching,
             back_button
         ),
     )
@@ -197,15 +199,15 @@ app_ui = ui.page_fluid(
 
 def server(input, output, session):
 
-    # Track which page to show
     current_page = reactive.Value("main_menu")
     
-    # Track button clicks
     plot_clicks = reactive.Value(0)
     match_clicks = reactive.Value(0)
     back_clicks = reactive.Value(0)
 
-    run_status = reactive.Value("Waiting for input...")
+    run_status_plot_spectra = reactive.Value("")
+    run_status_spec_lib_matching = reactive.Value("")
+
 
     @reactive.Effect
     def _():
@@ -220,6 +222,7 @@ def server(input, output, session):
             current_page.set("main_menu")
             back_clicks.set(input.back())
 
+
     @render.image
     def image():
         from pathlib import Path
@@ -228,6 +231,7 @@ def server(input, output, session):
         img: ImgData = {"src": str(dir / "www/emblem.png"), "width": "320px", "height": "250px"}
         return img
 
+
     @output
     @render.ui
     def main_ui():
@@ -310,8 +314,10 @@ def server(input, output, session):
         elif current_page() == "run_spec_lib_matching":
             return run_spec_lib_matching_ui(input.chromatography_platform())
 
+
+    '''
     @reactive.effect
-    @reactive.event(input.run_btn)
+    @reactive.event(input.run_btn_plot_spectra)
     def _():
         if current_page() == "plot_spectra":
             if len(input.spectrum_ID1())==0:
@@ -326,36 +332,71 @@ def server(input, output, session):
             if input.chromatography_platform() == "HRMS":
                 try:
                     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(), 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)
-                    plt.show()
-                    run_status.set(f"✅  Plotting has finished.")
+                    #plt.show()
+                    with io.BytesIO() as buf:
+                        plt.savefig(buf, format="png", dpi=150, bbox_inches="tight")
+                        yield buf.getvalue()
+                    run_status_plot_spectra.set(f"✅  Plotting has finished.")
                 except Exception as e:
-                    run_status.set(f"❌ Error: {traceback.format_exc()}")
+                    run_status_plot_spectra.set(f"❌ Error: {traceback.format_exc()}")
             elif input.chromatography_platform() == "NRMS":
                 try:
                     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)
-                    plt.show()
-                    run_status.set(f"✅  Plotting has finished.")
+                    #plt.show()
+                    run_status_plot_spectra.set(f"✅  Plotting has finished.")
                 except Exception as e:
-                    run_status.set(f"❌ Error: {traceback.format_exc()}")
+                    run_status_plot_spectra.set(f"❌ Error: {traceback.format_exc()}")
+
 
-        elif current_page() == 'run_spec_lib_matching':
+    @reactive.effect
+    @reactive.event(input.run_btn_run_spec_lib_matching)
+    def _():
+        if current_page() == 'run_spec_lib_matching':
             if input.chromatography_platform() == 'HRMS':
                 try:
                     run_spec_lib_matching_on_HRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], likely_reference_ids=None, 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(), 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(), n_top_matches_to_save=input.n_top_matches_to_save(), print_id_results=False, output_identification=f'{Path.cwd()}/output_identification.csv', output_similarity_scores=f'{Path.cwd()}/')
-                    run_status.set(f"✅  Spectral library matching has finished and results were written to {Path.cwd()}/output_similarity_scores.csv.")
+                    run_status_spec_lib_matching.set(f"✅  Spectral library matching has finished.")
                 except Exception as e:
-                    run_status.set(f"❌ Error: {traceback.format_exc()}")
+                    run_status_spec_lib_matching.set(f"❌ Error: {traceback.format_exc()}")
             elif input.chromatography_platform() == 'NRMS':
                 try:
                     run_spec_lib_matching_on_NRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], likely_reference_ids=None, 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(), n_top_matches_to_save=input.n_top_matches_to_save(), print_id_results=False, output_identification=f'{Path.cwd()}/output_identification.csv', output_similarity_scores=f'{Path.cwd()}/output_similarity_scores.csv')
-                    run_status.set(f"✅  Spectral library matching has finished and results were written to {Path.cwd()}/")
+                    run_status_spec_lib_matching.set(f"✅  Spectral library matching has finished.")
                 except Exception as e:
-                    run_status.set(f"❌ Error: {traceback.format_exc()}")
+                    run_status_spec_lib_matching.set(f"❌ Error: {traceback.format_exc()}")
+    '''
+
+
+    @render.download(filename=lambda: f"plot.png")
+    def run_btn_plot_spectra():
+        spectrum_ID1 = input.spectrum_ID1() or None
+        spectrum_ID2 = input.spectrum_ID2() or None
+
+        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(), 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)
+            #run_status_plot_spectra.set("✅ Plotting has finished.")
+        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)
+        with io.BytesIO() as buf:
+            fig.savefig(buf, format="png", dpi=150, bbox_inches="tight")
+            yield buf.getvalue()
+
+
+    @render.download(filename=lambda: f"plot.png")
+    def run_btn_spec_lib_matching():
+        if input.chromatography_platform() == "HRMS":
+            df_out = run_spec_lib_matching_on_HRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], likely_reference_ids=None, 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(), 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(), n_top_matches_to_save=input.n_top_matches_to_save(), print_id_results=False, output_identification=f'{Path.cwd()}/output_identification.csv', output_similarity_scores=f'{Path.cwd()}/', return_ID_output=True)
+        elif input.chromatography_platform() == "NRMS":
+            df_out = run_spec_lib_matching_on_NRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], likely_reference_ids=None, 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(), n_top_matches_to_save=input.n_top_matches_to_save(), print_id_results=False, output_identification=f'{Path.cwd()}/output_identification.csv', output_similarity_scores=f'{Path.cwd()}/output_similarity_scores.csv', return_ID_output=True)
+
+        df_out.to_csv(io.StringIO(), index=False)
+        return buf.getvalue().encode('utf-8')
 
 
     @render.text
     def status_output():
-        return run_status.get()
+        return run_status_plot_spectra.get()
+        return run_status_spec_lib_matching.get()
 
 
 

{pycompound-0.0.7 → pycompound-0.0.9}/src/pycompound/spec_lib_matching.py

@@ -389,7 +389,7 @@ def get_acc_NRMS(df_query, df_reference, unique_query_ids, unique_reference_ids,
 
 
 
-def run_spec_lib_matching_on_HRMS_data(query_data=None, reference_data=None, likely_reference_ids=None, similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, spectrum_preprocessing_order='FCNMWL', high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, window_size_centroiding=0.5, window_size_matching=0.5, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, n_top_matches_to_save=1, print_id_results=False, output_identification=None, output_similarity_scores=None):
+def run_spec_lib_matching_on_HRMS_data(query_data=None, reference_data=None, likely_reference_ids=None, similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, spectrum_preprocessing_order='FCNMWL', high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, window_size_centroiding=0.5, window_size_matching=0.5, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, n_top_matches_to_save=1, print_id_results=False, output_identification=None, output_similarity_scores=None, return_ID_output=False):
     '''
     runs spectral library matching on high-resolution mass spectrometry (HRMS) data
 
@@ -636,22 +636,26 @@ def run_spec_lib_matching_on_HRMS_data(query_data=None, reference_data=None, lik
     df_top_ref_specs.index = unique_query_ids
     df_top_ref_specs.index.names = ['Query Spectrum ID']
 
+    df_scores.columns = ['Reference Spectrum ID: ' + col for col in  list(map(str,df_scores.columns.tolist()))]
+
     # print the identification results if the user desires
     if print_id_results == True:
         print(df_top_ref_specs.to_string())
 
-    # write spectral library matching results to disk
-    df_top_ref_specs.to_csv(output_identification)
+    if return_ID_output is False:
+        # write spectral library matching results to disk
+        df_top_ref_specs.to_csv(output_identification)
 
-    # write all similarity scores to disk
-    df_scores.columns = ['Reference Spectrum ID: ' + col for col in  list(map(str,df_scores.columns.tolist()))]
-    df_scores.to_csv(output_similarity_scores)
+        # write all similarity scores to disk
+        df_scores.to_csv(output_similarity_scores)
+    else:
+        return df_top_ref_specs
 
 
 
 
 
-def run_spec_lib_matching_on_NRMS_data(query_data=None, reference_data=None, likely_reference_ids=None, spectrum_preprocessing_order='FNLW', similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, n_top_matches_to_save=1, print_id_results=False, output_identification=None, output_similarity_scores=None):
+def run_spec_lib_matching_on_NRMS_data(query_data=None, reference_data=None, likely_reference_ids=None, spectrum_preprocessing_order='FNLW', similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, n_top_matches_to_save=1, print_id_results=False, output_identification=None, output_similarity_scores=None, return_ID_output=False):
     '''
     runs spectral library matching on nominal-resolution mass spectrometry (NRMS) data
 
@@ -886,11 +890,15 @@ def run_spec_lib_matching_on_NRMS_data(query_data=None, reference_data=None, lik
     if print_id_results == True:
         print(df_top_ref_specs.to_string())
 
-    # write spectral library matching results to disk
-    df_top_ref_specs.to_csv(output_identification)
-
-    # write all similarity scores to disk
     df_scores.columns = ['Reference Spectrum ID: ' + col for col in  list(map(str,df_scores.columns.tolist()))]
-    df_scores.to_csv(output_similarity_scores)
 
+    if return_ID_output is False:
+        # write spectral library matching results to disk
+        df_top_ref_specs.to_csv(output_identification)
+
+        # write all similarity scores to disk
+        df_scores.columns = ['Reference Spectrum ID: ' + col for col in  list(map(str,df_scores.columns.tolist()))]
+        df_scores.to_csv(output_similarity_scores)
+    else:
+        return df_top_ref_specs
 

{pycompound-0.0.7 → pycompound-0.0.9}/src/pycompound.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycompound
-Version: 0.0.7
+Version: 0.0.9
 Summary: Python package to perform compound identification in mass spectrometry via spectral library matching.
 Author-email: Hunter Dlugas <fy7392@wayne.edu>
 License-Expression: MIT
@@ -19,6 +19,7 @@ Requires-Dist: pyteomics==4.7.2
 Requires-Dist: netCDF4==1.6.5
 Requires-Dist: lxml>=5.1.0
 Requires-Dist: orjson==3.11.0
+Requires-Dist: shiny==1.4.0
 Requires-Dist: joblib==1.5.2
 Dynamic: license-file
 

{pycompound-0.0.7 → pycompound-0.0.9}/src/pycompound.egg-info/requires.txt

@@ -6,4 +6,5 @@ pyteomics==4.7.2
 netCDF4==1.6.5
 lxml>=5.1.0
 orjson==3.11.0
+shiny==1.4.0
 joblib==1.5.2

{pycompound-0.0.7 → pycompound-0.0.9}/src/pycompound.egg-info/top_level.txt

@@ -1,3 +1,4 @@
 app
 pycompound
+rsconnect-python
 www