apscale-gui 3.2.2__tar.gz → 3.2.4__tar.gz

{apscale_gui-3.2.2/apscale_gui.egg-info → apscale_gui-3.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apscale_gui
-Version: 3.2.2
+Version: 3.2.4
 Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
 Home-page: https://github.com/TillMacher/apscale_gui
 Author: Till-Hendrik Macher

{apscale_gui-3.2.2 → apscale_gui-3.2.4}/apscale_gui/apscale_gui.py

@@ -373,11 +373,32 @@ def update_settings_file(settings_xlsx, settings_dfs):
 
     st.success(f"Settings updated and saved to {settings_xlsx}")
 
-def run_apscale(task, project_folder):
+def run_apscale(task, project_folder, modules_to_run):
 
     st.info('Starting apscale analysis! Please refer to the terminal for live outputs!')
     print('')
 
+    if modules_to_run != []:
+        for task in modules_to_run:
+            if task == "PE-merging":
+                b_pe_merging.main(project_folder)
+            elif task == "Primer-trimming":
+                c_primer_trimming.main(project_folder)
+            elif task == "Quality-filtering":
+                d_quality_filtering.main(project_folder)
+            elif task == "Dereplication":
+                e_dereplication.main(project_folder)
+            elif task == "Denoising":
+                f_denoising.main(project_folder)
+            elif task == "SWARM clustering":
+                g_swarm_clustering.main(project_folder)
+            elif task == "Replicate merging":
+                h_replicate_merging.main(project_folder)
+            elif task == "NC removal":
+                i_nc_removal.main(project_folder)
+            elif task == "Generate read table":
+                j_generate_read_table.main(project_folder)
+
     if task == "Run apscale (basic mode)":
         b_pe_merging.main(project_folder)
         c_primer_trimming.main(project_folder)
@@ -386,7 +407,7 @@ def run_apscale(task, project_folder):
         f_denoising.main(project_folder)
         g_swarm_clustering.main(project_folder)
         j_generate_read_table.main(project_folder)
-    if task == "Run apscale (complete mode)":
+    elif task == "Run apscale (complete mode)":
         b_pe_merging.main(project_folder)
         c_primer_trimming.main(project_folder)
         d_quality_filtering.main(project_folder)
@@ -396,27 +417,29 @@ def run_apscale(task, project_folder):
         h_replicate_merging.main(project_folder)
         i_nc_removal.main(project_folder)
         j_generate_read_table.main(project_folder)
-    if task == "PE-merging":
+    elif task == "PE-merging":
         b_pe_merging.main(project_folder)
-    if task == "Primer-trimming":
+    elif task == "Primer-trimming":
         c_primer_trimming.main(project_folder)
-    if task == "Quality-filtering":
+    elif task == "Quality-filtering":
         d_quality_filtering.main(project_folder)
-    if task == "Dereplication":
+    elif task == "Dereplication":
         e_dereplication.main(project_folder)
-    if task == "Denoising":
+    elif task == "Denoising":
         f_denoising.main(project_folder)
-    if task == "SWARM clustering":
+    elif task == "SWARM clustering":
         g_swarm_clustering.main(project_folder)
-    if task == "Replicate merging":
+    elif task == "Replicate merging":
         h_replicate_merging.main(project_folder)
-    if task == "NC removal":
+    elif task == "NC removal":
         i_nc_removal.main(project_folder)
-    if task == "Generate read table":
+    elif task == "Generate read table":
         j_generate_read_table.main(project_folder)
 
     st.success('Finished apscale analysis!')
     print('')
+    print('Finished apscale analysis!')
+    print('')
 
 def run_apscale_blast(project_folder, available_fasta_files, available_databases):
 
@@ -449,8 +472,7 @@ def run_apscale_blast(project_folder, available_fasta_files, available_databases
 
     categories = ['t_species', 't_genus', 't_family', 't_order', 't_class']
     thresholds = ','.join([str(st.session_state[i]) for i in categories])
-    filter_mode = 1
-    b_filter(output_folder, database, thresholds, str(st.session_state['n_cores']), filter_mode, st.session_state['rating_range'])
+    b_filter(output_folder, database, thresholds, str(st.session_state['n_cores']), st.session_state["filter_mode"], st.session_state['rating_range'], st.session_state['sim_range'])
 
     st.success('Finished blastn!')
     print('')
@@ -938,12 +960,28 @@ def main():
                 ############################################################################################################
                 st.subheader('Run apscale')
                 options = ['Run apscale (basic mode)', 'Run apscale (complete mode)', 'PE-merging', 'Primer-trimming', 'Quality-filtering', 'Dereplication', 'Denoising', 'SWARM clustering', 'Replicate merging', 'NC removal', 'Generate read table']
-                st.selectbox(label='Select module to run', options=options, index=0, key='run_apscale_mode')
+                col1, col2 = st.columns(2)
+                with col1:
+                    run_mode = st.selectbox(label='Select module to run', options=options, index=0, key='run_apscale_mode')
+                with col2:
+                    selected_module = False
+                    modules_to_run = []
+                    if run_mode not in ['Run apscale (basic mode)', 'Run apscale (complete mode)']:
+                        selected_module = st.selectbox(label='Select module(s) to run', options=['Run all following modules', 'Run selected module only'], key='run_apscale_mode_continous')
+                        if selected_module == 'Run all following modules':
+                            selected_module_basic = st.selectbox(label='Run in basic mode', options=['Yes', 'No'], key='selected_module_basic')
+                if selected_module == 'Run all following modules':
+                    module_loc = options.index(run_mode)
+                    modules_to_run = options[module_loc:]
+                    if selected_module_basic == 'Yes':
+                        modules_to_run = [i for i in modules_to_run if i not in ['Replicate merging', 'NC removal']]
+                    modules_disp = ' -> '.join(modules_to_run)
+                    st.info(f'All following modules will be run:\n\n{modules_disp}')
 
                 if st.session_state["P5 Primer (5' - 3')"] == '' or st.session_state["P7 Primer (5' - 3')"] == '' or st.session_state['min length'] == '' or st.session_state['max length'] =='':
                     st.error('Please fill out all required fields!')
                 elif float(st.session_state["sequence group threshold"]) >= 1:
-                    st.error('Please choose a sequence group threshold > 1.\n\nESVs are generated seperately!')
+                    st.error('Please choose a sequence group threshold between 0 and 0.99.\n\nESVs are generated seperately!')
                 else:
                     if st.session_state['run_apscale_mode'] == 'Run apscale (basic mode)':
                         st.info('The "Basic mode" mode skips "Replicate merging" and "NC removal".')
@@ -951,7 +989,7 @@ def main():
                         st.info('The "Complete mode" runs all modules (except specifically disabled above).')
                     if st.button('Start raw data analysis'):
                         update_settings_file(settings_xlsx, settings_dfs)
-                        run_apscale(st.session_state['run_apscale_mode'], project_folder)
+                        run_apscale(st.session_state['run_apscale_mode'], project_folder, modules_to_run)
 
 
                 ############################################################################################################
@@ -965,7 +1003,7 @@ def main():
                     st.text_input(label='n_cores', key='n_cores', value=multiprocessing.cpu_count()-2)
                     st.text_input(label='subset_size', key='subset_size', value=100)
                 with col2:
-                    st.selectbox(label='Task', key='task', options=['blastn', 'megablast', 'dc-megablast'])
+                    st.selectbox(label='Task', key='task', options=['blastn', 'megablast', 'dc-megablast'], index=1)
                     st.text_input(label='max_target_seqs', key='max_target_seqs', value=20)
                 # Database & query
                 available_databases = {Path(i).name:Path(i) for i in glob.glob(str(path_to_projects / 'APSCALE_databases' / '*'))}
@@ -984,7 +1022,11 @@ def main():
                         st.text_input(label='Order (%)', key='t_order', value=87)
                     with col2:
                         st.selectbox(label='Masking', key='masking', options=[True, False], index=0)
-                        st.text_input(label='Rating range', key='rating_range', value=10)
+                        filter_mode_dict = {'similarity -> e-value -> rating (optional)':"1", 'e-value -> similarity -> rating (optional)':"2", 'similarity -> rating (optional)':"3"}
+                        filter_mode_key = st.selectbox(label='Filter mode', key='filter_mode_key', options=filter_mode_dict.keys())
+                        st.session_state["filter_mode"] = filter_mode_dict[filter_mode_key]
+                        st.selectbox(label='Rating range', key='rating_range', options=[i for i in range(0, 11)], index=5)
+                        st.selectbox(label='Similarity range', key='sim_range', options=[i for i in range(0, 11)], index=0)
                 # Run blast
                 st.subheader('Run apscale-blast')
                 if st.button(f'Start taxonomic assignment'):

{apscale_gui-3.2.2 → apscale_gui-3.2.4/apscale_gui.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apscale_gui
-Version: 3.2.2
+Version: 3.2.4
 Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
 Home-page: https://github.com/TillMacher/apscale_gui
 Author: Till-Hendrik Macher

{apscale_gui-3.2.2 → apscale_gui-3.2.4}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="apscale_gui",
-    version="3.2.2",
+    version="3.2.4",
     author="Till-Hendrik Macher",
     author_email="macher@uni-trier.de",
     description="Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface",