2024-10-23 bug changes (#23)

vanallenlab · Oct 25, 2024 · 5b40001 · 5b40001
1 parent 20ee1e3
commit 5b40001
Show file tree

Hide file tree

Showing 12 changed files with 1,017 additions and 104 deletions.
diff --git a/example_output/example.log b/example_output/example.log
diff --git a/moalmanac/annotation-databases.ini b/moalmanac/annotation-databases.ini
@@ -1,4 +1,4 @@
-[databases]
+[paths]
 root = ../datasources
 almanac_handle = ${root}/moalmanac/molecular-oncology-almanac.json
 cancerhotspots_handle = ${root}/cancerhotspots/hotspots_v2.txt

diff --git a/moalmanac/config.ini b/moalmanac/config.ini
@@ -8,10 +8,12 @@ include_model_similarity_in_actionability_report = on
 include_preclinical_efficacy_in_actionability_report = on
 
 [logging]
+; Possible values for level include "NOTSET", "DEBUG", "INFO", "WARNING", "ERROR", and "CRITICAL". They are described
+; within the logging module's document: https://docs.python.org/3/library/logging.html#logging-levels.
 level = INFO
 
 [versions]
-interpreter = 0.7.1
+interpreter = 0.7.2
 database = v.2024-04-11
 
 [exac]

diff --git a/moalmanac/logger.py b/moalmanac/logger.py
@@ -1,6 +1,7 @@
 import json
 import logging
 
+
 class Logger:
     @staticmethod
     def generate_filename(folder, label):
@@ -16,6 +17,7 @@ def setup(cls, output_folder, file_prefix, config):
             level=config['logging']['level']
         )
 
+
 class Messages:
     @staticmethod
     def dataframe_size(label, dataframe, add_line_break=False):

diff --git a/moalmanac/moalmanac.py b/moalmanac/moalmanac.py
@@ -333,7 +333,7 @@ def somatic_variants(df, dbs, ontology, config, path_validation):
                 logger.Messages.general(message="No passed validation sequencing variants to annotate with")
         else:
             logger.Messages.general(message="No somatic variants detected. Skipping annotation and evaluation.")
-            evaluated= features.Features.create_empty_dataframe()
+            evaluated = features.Features.create_empty_dataframe()
         logger.Messages.general(message="Annotation and evaluation of somatic variants complete", add_line_break=True)
         return evaluated
 
@@ -706,8 +706,6 @@ def main(patient, inputs, output_folder, config, dbs, dbs_preclinical=None):
 
 
 if __name__ == "__main__":
-    start_time = time.time()
-
     arg_parser = argparse.ArgumentParser(
         prog='Molecular Oncology Almanac',
         description='A clinical interpretation algorithm for cancer genomics.'
@@ -854,21 +852,19 @@ def main(patient, inputs, output_folder, config, dbs, dbs_preclinical=None):
     config_ini = Ini.read(args.config, extended_interpolation=False, convert_to_dictionary=False)
 
     db_paths = Ini.read(args.dbs, extended_interpolation=True, convert_to_dictionary=True)
+    db_paths = db_paths['paths']
+
     if args.preclinical_dbs:
         preclinical_db_paths = Ini.read(args.preclinical_dbs, extended_interpolation=True, convert_to_dictionary=True)
+        preclinical_db_paths = preclinical_db_paths['paths']
     else:
         preclinical_db_paths = None
 
-    print(db_paths)
     main(
         patient=patient_dict,
         inputs=inputs_dict,
         output_folder=output_directory,
         config=config_ini,
-        dbs=db_paths['databases'],
-        dbs_preclinical=preclinical_db_paths['preclinical']
+        dbs=db_paths,
+        dbs_preclinical=preclinical_db_paths
     )
-
-    end_time = time.time()
-    time_statement = "Molecular Oncology Almanac runtime: %s seconds" % round((end_time - start_time), 4)
-    print(time_statement)
diff --git a/moalmanac/preclinical-databases.ini b/moalmanac/preclinical-databases.ini
@@ -1,4 +1,4 @@
-[preclinical]
+[paths]
 root = ../datasources
 almanac_gdsc_mappings = ${root}/preclinical/formatted/almanac-gdsc-mappings.json
 summary = ${root}/preclinical/formatted/cell-lines.summary.txt

diff --git a/moalmanac/run_example.py b/moalmanac/run_example.py
@@ -45,12 +45,15 @@
 }
 
 config_ini_path = "config.ini"
-dbs_ini_path = "annotation-databases.ini"
-dbs_preclinical_ini_path = "preclinical-databases.ini"
-
 config_ini = Ini.read(config_ini_path, extended_interpolation=False, convert_to_dictionary=False)
+
+dbs_ini_path = "annotation-databases.ini"
 db_paths = Ini.read(dbs_ini_path, extended_interpolation=True, convert_to_dictionary=True)
+db_paths = db_paths['paths']
+
+dbs_preclinical_ini_path = "preclinical-databases.ini"
 preclinical_db_paths = Ini.read(dbs_preclinical_ini_path, extended_interpolation=True, convert_to_dictionary=True)
+preclinical_db_paths = preclinical_db_paths['paths']
 
 
 def execute_cmd(command):
@@ -71,8 +74,8 @@ def execute_cmd(command):
     inputs=input_dictionary,
     output_folder=output_directory,
     config=config_ini,
-    dbs=db_paths['databases'],
-    dbs_preclinical=preclinical_db_paths['preclinical']
+    dbs=db_paths,
+    dbs_preclinical=preclinical_db_paths
 )
 end_time = time.time()
 

diff --git a/moalmanac/simplified_input.py b/moalmanac/simplified_input.py
@@ -300,8 +300,8 @@ def main(patient, input_file, output_folder, config, dbs, dbs_preclinical=None):
         input_file=args.input,
         output_folder=output_directory,
         config=config_ini,
-        dbs=db_paths,
-        dbs_preclinical=preclinical_db_paths
+        dbs=db_paths['databases'],
+        dbs_preclinical=preclinical_db_paths['preclinical'] if preclinical_db_paths else None
     )
 
     end_time = time.time()

diff --git a/moalmanac/templates/report_table/table_biological.html b/moalmanac/templates/report_table/table_biological.html
@@ -7,12 +7,14 @@ <h4 class="panel-title">Variants and Features that may be Biologically Relevant<
         <table class="table table-hover table-striped table-condensed">
             {% include 'report_table/columns_biological.html' %}
             <tbody>
-                {% for label, group in report.alterations[report.alterations['score_bin'] == 'Biologically Relevant'].groupby('feature_type') %}
-                <tr>
-                    <td>{{ label }}</td>
-                    <td>{{ ', '.join(group['feature_display'].sort_values().tolist()) }}</td>
-                </tr>
-                {% endfor %}
+                {% if not report.alterations.empty %}
+                    {% for label, group in report.alterations[report.alterations['score_bin'] == 'Biologically Relevant'].groupby('feature_type') %}
+                    <tr>
+                        <td>{{ label }}</td>
+                        <td>{{ ', '.join(group['feature_display'].sort_values().tolist()) }}</td>
+                    </tr>
+                    {% endfor %}
+                {% endif %}
             </tbody>
         </table>
     </div>

diff --git a/moalmanac/templates/report_table/table_prognostic.html b/moalmanac/templates/report_table/table_prognostic.html
@@ -7,31 +7,33 @@ <h4 class="panel-title">Variants and Features associated with Prognostic Informa
         <table class="table table-hover table-striped table-condensed">
             {% include 'report_table/columns_prognosis.html' %}
             <tbody>
-                {% for index in report.alterations[report.alterations['prognostic_predictive_implication'].notnull()].sort_values(['prognostic_predictive_implication_map', 'prognostic_score_bin_map'], ascending=[False, False]).index.tolist() %}
-                <tr>
-                    <td>{{ report.alterations.loc[index, 'prognostic_predictive_implication'] }}
-                        <br>
-                        {{ report.alterations.loc[index, 'prognostic_score_bin'] }}
-                        <br>
-                        {% include 'modals/evidence_prognosis.html' %}
-                    <td>{{ report.alterations.loc[index, 'feature_type'] }}</td>
-                    <td>{{ report.alterations.loc[index, 'feature_display'] }}</td>
-                    <td>
-                        {% if report.alterations.loc[index, 'favorable_prognosis'] == 1.0 %}
-                            Favorable
-                        {% else %}
-                            Not favorable
-                        {% endif %}
-                        <br>
-                        {{ report.alterations.loc[index, 'prognostic_description'] }}
-                        {% if report.alterations.loc[index, 'prognostic_url'] != "" %}
-                            <a href="{{ report.alterations.loc[index, 'prognostic_url'] }}" target="_blank">
-                                [source]
-                            </a>
-                        {% endif %}
-                    </td>
-                </tr>
-                {% endfor %}
+                {% if not report.alterations.empty %}
+                    {% for index in report.alterations[report.alterations['prognostic_predictive_implication'].notnull()].sort_values(['prognostic_predictive_implication_map', 'prognostic_score_bin_map'], ascending=[False, False]).index.tolist() %}
+                    <tr>
+                        <td>{{ report.alterations.loc[index, 'prognostic_predictive_implication'] }}
+                            <br>
+                            {{ report.alterations.loc[index, 'prognostic_score_bin'] }}
+                            <br>
+                            {% include 'modals/evidence_prognosis.html' %}
+                        <td>{{ report.alterations.loc[index, 'feature_type'] }}</td>
+                        <td>{{ report.alterations.loc[index, 'feature_display'] }}</td>
+                        <td>
+                            {% if report.alterations.loc[index, 'favorable_prognosis'] == 1.0 %}
+                                Favorable
+                            {% else %}
+                                Not favorable
+                            {% endif %}
+                            <br>
+                            {{ report.alterations.loc[index, 'prognostic_description'] }}
+                            {% if report.alterations.loc[index, 'prognostic_url'] != "" %}
+                                <a href="{{ report.alterations.loc[index, 'prognostic_url'] }}" target="_blank">
+                                    [source]
+                                </a>
+                            {% endif %}
+                        </td>
+                    </tr>
+                    {% endfor %}
+                {% endif %}
             </tbody>
         </table>
     </div>

diff --git a/moalmanac/templates/report_table/table_resistance.html b/moalmanac/templates/report_table/table_resistance.html
@@ -7,31 +7,33 @@ <h4 class="panel-title">Variants and Features associated with Therapeutic Resist
         <table class="table table-hover table-striped table-condensed">
             {% include 'report_table/columns_therapies.html' %}
             <tbody>
-                {% for index in report.alterations[report.alterations['resistance_predictive_implication'].notnull()].sort_values(['resistance_predictive_implication_map', 'resistance_score_bin_map'], ascending=[False, False]).index.tolist() %}
-                <tr>
-                    <td>{{ report.alterations.loc[index, 'resistance_predictive_implication'] }}
-                        <br>
-                        {{ report.alterations.loc[index, 'resistance_score_bin'] }}
-                        <br>
-                        {% include 'modals/evidence_resistance.html' %}
-                    <td>{{ report.alterations.loc[index, 'feature_type'] }}</td>
-                    <td>{{ report.alterations.loc[index, 'feature_display'] }}</td>
-                    <td>
-                        {% if report.alterations.loc[index, 'resistance_therapy_name'] != '' %}
-                            {{ report.alterations.loc[index, 'resistance_therapy_name'] }}
-                        {% else %}
-                            {{ report.alterations.loc[index, 'resistance_therapy_type'] }}
-                        {% endif %}
-                        <br>
-                        {{ report.alterations.loc[index, 'resistance_description'] }}
-                        {% if report.alterations.loc[index, 'resistance_url'] != "" %}
-                            <a href="{{ report.alterations.loc[index, 'resistance_url'] }}" target="_blank">
-                                [source]
-                            </a>
-                        {% endif %}
-                    </td>
-                </tr>
-                {% endfor %}
+                {% if not report.alterations.empty %}
+                    {% for index in report.alterations[report.alterations['resistance_predictive_implication'].notnull()].sort_values(['resistance_predictive_implication_map', 'resistance_score_bin_map'], ascending=[False, False]).index.tolist() %}
+                    <tr>
+                        <td>{{ report.alterations.loc[index, 'resistance_predictive_implication'] }}
+                            <br>
+                            {{ report.alterations.loc[index, 'resistance_score_bin'] }}
+                            <br>
+                            {% include 'modals/evidence_resistance.html' %}
+                        <td>{{ report.alterations.loc[index, 'feature_type'] }}</td>
+                        <td>{{ report.alterations.loc[index, 'feature_display'] }}</td>
+                        <td>
+                            {% if report.alterations.loc[index, 'resistance_therapy_name'] != '' %}
+                                {{ report.alterations.loc[index, 'resistance_therapy_name'] }}
+                            {% else %}
+                                {{ report.alterations.loc[index, 'resistance_therapy_type'] }}
+                            {% endif %}
+                            <br>
+                            {{ report.alterations.loc[index, 'resistance_description'] }}
+                            {% if report.alterations.loc[index, 'resistance_url'] != "" %}
+                                <a href="{{ report.alterations.loc[index, 'resistance_url'] }}" target="_blank">
+                                    [source]
+                                </a>
+                            {% endif %}
+                        </td>
+                    </tr>
+                    {% endfor %}
+                {% endif %}
             </tbody>
         </table>
     </div>

diff --git a/moalmanac/templates/report_table/table_sensitive.html b/moalmanac/templates/report_table/table_sensitive.html
@@ -7,34 +7,35 @@ <h4 class="panel-title">Variants and Features associated with Therapeutic Sensit
         <table class="table table-hover table-striped table-condensed">
             {% include 'report_table/columns_therapies.html' %}
             <tbody>
-                {% for index in report.alterations[report.alterations['sensitive_predictive_implication'].notnull()].sort_values(['sensitive_predictive_implication_map', 'sensitive_score_bin_map'], ascending=[False, False]).index.tolist() %}
-
-                <tr>
-                    <td>{{ report.alterations.loc[index, 'sensitive_predictive_implication'] }}
-                        <br>
-                        {{ report.alterations.loc[index, 'sensitive_score_bin'] }}
-                        <br>
-                        {% include 'modals/evidence_sensitive.html' %}
-                    </td>
-                    <td>{{ report.alterations.loc[index, 'feature_type'] }}</td>
-                    <td>{{ report.alterations.loc[index, 'feature_display'] }}
-                    <td>
-                        {% if report.alterations.loc[index, 'sensitive_therapy_name'] != '' %}
-                            {{ report.alterations.loc[index, 'sensitive_therapy_name'] }}
-                        {% else %}
-                            {{ report.alterations.loc[index, 'sensitive_therapy_type'] }}
-                        {% endif %}
-                        <br>
-                        {{ report.alterations.loc[index, 'sensitive_description'] }}
-                        {% if report.alterations.loc[index, 'sensitive_url'] != "" %}
-                            <a href="{{ report.alterations.loc[index, 'sensitive_url'] }}" target="_blank">
-                                [source]
-                            </a>
-                        {% endif %}
-                        {% include 'modals/efficacy.html' %}
-                    </td>
-                </tr>
-                {% endfor %}
+                {% if not report.alterations.empty %}
+                    {% for index in report.alterations[report.alterations['sensitive_predictive_implication'].notnull()].sort_values(['sensitive_predictive_implication_map', 'sensitive_score_bin_map'], ascending=[False, False]).index.tolist() %}
+                    <tr>
+                        <td>{{ report.alterations.loc[index, 'sensitive_predictive_implication'] }}
+                            <br>
+                            {{ report.alterations.loc[index, 'sensitive_score_bin'] }}
+                            <br>
+                            {% include 'modals/evidence_sensitive.html' %}
+                        </td>
+                        <td>{{ report.alterations.loc[index, 'feature_type'] }}</td>
+                        <td>{{ report.alterations.loc[index, 'feature_display'] }}
+                        <td>
+                            {% if report.alterations.loc[index, 'sensitive_therapy_name'] != '' %}
+                                {{ report.alterations.loc[index, 'sensitive_therapy_name'] }}
+                            {% else %}
+                                {{ report.alterations.loc[index, 'sensitive_therapy_type'] }}
+                            {% endif %}
+                            <br>
+                            {{ report.alterations.loc[index, 'sensitive_description'] }}
+                            {% if report.alterations.loc[index, 'sensitive_url'] != "" %}
+                                <a href="{{ report.alterations.loc[index, 'sensitive_url'] }}" target="_blank">
+                                    [source]
+                                </a>
+                            {% endif %}
+                            {% include 'modals/efficacy.html' %}
+                        </td>
+                    </tr>
+                    {% endfor %}
+                {% endif %}
             </tbody>
         </table>
     </div>