gsMap 1.67__py3-none-any.whl → 1.70__py3-none-any.whl

gsMap/report.py

@@ -1,160 +1,160 @@
-import logging
-import os
-import shutil
-
-import pandas as pd
-from jinja2 import Environment, FileSystemLoader
-
-import gsMap
-from gsMap.cauchy_combination_test import run_Cauchy_combination
-from gsMap.config import CauchyCombinationConfig, ReportConfig
-from gsMap.diagnosis import run_Diagnosis
-
-logger = logging.getLogger(__name__)
-
-# Load the Jinja2 environment
-try:
-    from importlib.resources import files
-
-    template_dir = files('gsMap').joinpath('templates')
-except (ImportError, FileNotFoundError):
-    # Fallback to a relative path if running in development mode
-    template_dir = os.path.join(os.path.dirname(__file__), 'templates')
-
-# Set up Jinja2 environment
-env = Environment(loader=FileSystemLoader(template_dir))
-
-# Load the template
-template = env.get_template('report_template.html')
-
-def copy_files_to_report_dir(result_dir, report_dir, files_to_copy):
-    """Copy specified files (HTML or PNG) to the report directory."""
-    os.makedirs(report_dir, exist_ok=True)
-    for file in files_to_copy:
-        shutil.copy2(file, os.path.join(report_dir, os.path.basename(file)))
-
-
-def load_cauchy_table(csv_file):
-    """Load the Cauchy combination table from a compressed CSV file using Pandas."""
-    df = pd.read_csv(csv_file, compression='gzip')
-    table_data = df[['annotation', 'p_cauchy', 'p_median']].to_dict(orient='records')
-    return table_data
-
-
-def load_gene_diagnostic_info(csv_file):
-    """Load the Gene Diagnostic Info CSV file and return the top 50 rows."""
-    df = pd.read_csv(csv_file)
-    top_50 = df.head(50).to_dict(orient='records')
-    return top_50
-
-
-def embed_html_content(file_path):
-    """Read the content of an HTML file and return it as a string."""
-    with open(file_path, 'r') as f:
-        return f.read()
-
-def check_and_run_cauchy_combination(config):
-    cauchy_result_file = config.get_cauchy_result_file(config.trait_name)
-    if cauchy_result_file.exists():
-        logger.info(
-            f"Cauchy combination already done for trait {config.trait_name}. Results saved at {cauchy_result_file}. Skipping...")
-    else:
-        logger.info(f"Running Cauchy combination for trait {config.trait_name}...")
-        cauchy_config = CauchyCombinationConfig(
-            workdir=config.workdir,
-            sample_name=config.sample_name,
-            annotation=config.annotation,
-            trait_name=config.trait_name,
-        )
-        run_Cauchy_combination(cauchy_config)
-
-    df = pd.read_csv(cauchy_result_file, compression='gzip')
-    table_data = df[['annotation', 'p_cauchy', 'p_median']].to_dict(orient='records')
-
-    return table_data
-
-def run_report(config: ReportConfig, run_parameters=None):
-
-    logger.info('Running gsMap Diagnosis Module')
-    run_Diagnosis(config)
-    logger.info('gsMap Diagnosis running successfully')
-
-    report_dir = config.get_report_dir(config.trait_name)
-    gene_diagnostic_info_file = config.get_gene_diagnostic_info_save_path(config.trait_name)
-    gene_diagnostic_info = load_gene_diagnostic_info(gene_diagnostic_info_file)
-
-    # Load data (Cauchy table and gene diagnostic info)
-    cauchy_table = check_and_run_cauchy_combination(config)
-
-    # Paths to PNGs for gene expression and GSS distribution
-    gss_distribution_dir = config.get_GSS_plot_dir(config.trait_name)
-
-    gene_plots = []
-    plot_select_gene_list = config.get_GSS_plot_select_gene_file(config.trait_name).read_text().splitlines()
-    for gene_name in plot_select_gene_list:
-        expression_png = gss_distribution_dir / f"{config.sample_name}_{gene_name}_Expression_Distribution.png"
-        gss_png = gss_distribution_dir / f"{config.sample_name}_{gene_name}_GSS_Distribution.png"
-        # check if expression and GSS plots exist
-        if not os.path.exists(expression_png) or not os.path.exists(gss_png):
-            print(f"Skipping gene {gene_name} as expression or GSS plot is missing.")
-            continue
-        gene_plots.append({
-            'name': gene_name,
-            'expression_plot': expression_png.relative_to(report_dir),  # Path for gene expression plot
-            'gss_plot': gss_png.relative_to(report_dir)  # Path for GSS distribution plot
-        })
-
-    # # Copy PNG files to the report directory
-    # copy_files_to_report_dir(result_dir, report_dir, [gene['expression_plot'] for gene in gene_plots] + [gene['gss_plot'] for gene in gene_plots])
-
-    # Update paths to point to copied images inside the report folder
-    # for gene in gene_plots:
-    #     gene['expression_plot'] = os.path.join(os.path.basename(gene['expression_plot']))
-    #     gene['gss_plot'] = os.path.join(os.path.basename(gene['gss_plot']))
-
-    # Sample data for other report components
-    title = f"{config.sample_name} Genetic Spatial Mapping Report"
-
-    genetic_mapping_plot = embed_html_content(config.get_gsMap_html_plot_save_path(config.trait_name))
-    manhattan_plot = embed_html_content(config.get_manhattan_html_plot_path(config.trait_name))
-
-    gsmap_version = gsMap.__version__
-    # Render the template with dynamic content, including the run parameters
-
-    trait_name = config.trait_name
-    default_run_parameters = {
-        "Sample Name": config.sample_name,
-        "Trait Name": trait_name,
-        "Summary Statistics File": config.sumstats_file,
-        "HDF5 Path": config.hdf5_with_latent_path,
-        "Annotation": config.annotation,
-        "Spatial LDSC Save Directory": config.ldsc_save_dir,
-        "Cauchy Directory": config.cauchy_save_dir,
-        "Report Directory": config.get_report_dir(trait_name),
-        "gsMap Report File": config.get_gsMap_report_file(trait_name),
-        "Gene Diagnostic Info File": config.get_gene_diagnostic_info_save_path(trait_name),
-        "Report Generation Date": pd.Timestamp.now().strftime('%Y-%m-%d %H:%M:%S'),
-    }
-
-    if run_parameters is not None:
-        default_run_parameters.update(run_parameters)
-
-
-    output_html = template.render(
-        title=title,
-        genetic_mapping_plot=genetic_mapping_plot,  # Inlined genetic mapping plot
-        manhattan_plot=manhattan_plot,  # Inlined Manhattan plot
-        cauchy_table=cauchy_table,
-        gene_plots=gene_plots,  # List of PNG paths for gene plots
-        gsmap_version=gsmap_version,
-        parameters=default_run_parameters,  # Pass the run parameters to the template
-        gene_diagnostic_info=gene_diagnostic_info  # Include top 50 gene diagnostic info rows
-    )
-
-    # Save the generated HTML report in the 'report' directory
-    report_file = config.get_gsMap_report_file(config.trait_name)
-    with open(report_file, "w") as f:
-        f.write(output_html)
-
-    logger.info(f"Report generated successfully! Saved at {report_file}.")
-    logger.info(f"Copy the report directory to your local PC and open the HTML report file in a web browser to view the report.")
+import logging
+import os
+import shutil
+
+import pandas as pd
+from jinja2 import Environment, FileSystemLoader
+
+import gsMap
+from gsMap.cauchy_combination_test import run_Cauchy_combination
+from gsMap.config import CauchyCombinationConfig, ReportConfig
+from gsMap.diagnosis import run_Diagnosis
+
+logger = logging.getLogger(__name__)
+
+# Load the Jinja2 environment
+try:
+    from importlib.resources import files
+
+    template_dir = files('gsMap').joinpath('templates')
+except (ImportError, FileNotFoundError):
+    # Fallback to a relative path if running in development mode
+    template_dir = os.path.join(os.path.dirname(__file__), 'templates')
+
+# Set up Jinja2 environment
+env = Environment(loader=FileSystemLoader(template_dir))
+
+# Load the template
+template = env.get_template('report_template.html')
+
+def copy_files_to_report_dir(result_dir, report_dir, files_to_copy):
+    """Copy specified files (HTML or PNG) to the report directory."""
+    os.makedirs(report_dir, exist_ok=True)
+    for file in files_to_copy:
+        shutil.copy2(file, os.path.join(report_dir, os.path.basename(file)))
+
+
+def load_cauchy_table(csv_file):
+    """Load the Cauchy combination table from a compressed CSV file using Pandas."""
+    df = pd.read_csv(csv_file, compression='gzip')
+    table_data = df[['annotation', 'p_cauchy', 'p_median']].to_dict(orient='records')
+    return table_data
+
+
+def load_gene_diagnostic_info(csv_file):
+    """Load the Gene Diagnostic Info CSV file and return the top 50 rows."""
+    df = pd.read_csv(csv_file)
+    top_50 = df.head(50).to_dict(orient='records')
+    return top_50
+
+
+def embed_html_content(file_path):
+    """Read the content of an HTML file and return it as a string."""
+    with open(file_path, 'r') as f:
+        return f.read()
+
+def check_and_run_cauchy_combination(config):
+    cauchy_result_file = config.get_cauchy_result_file(config.trait_name)
+    if cauchy_result_file.exists():
+        logger.info(
+            f"Cauchy combination already done for trait {config.trait_name}. Results saved at {cauchy_result_file}. Skipping...")
+    else:
+        logger.info(f"Running Cauchy combination for trait {config.trait_name}...")
+        cauchy_config = CauchyCombinationConfig(
+            workdir=config.workdir,
+            sample_name=config.sample_name,
+            annotation=config.annotation,
+            trait_name=config.trait_name,
+        )
+        run_Cauchy_combination(cauchy_config)
+
+    df = pd.read_csv(cauchy_result_file, compression='gzip')
+    table_data = df[['annotation', 'p_cauchy', 'p_median']].to_dict(orient='records')
+
+    return table_data
+
+def run_report(config: ReportConfig, run_parameters=None):
+
+    logger.info('Running gsMap Diagnosis Module')
+    run_Diagnosis(config)
+    logger.info('gsMap Diagnosis running successfully')
+
+    report_dir = config.get_report_dir(config.trait_name)
+    gene_diagnostic_info_file = config.get_gene_diagnostic_info_save_path(config.trait_name)
+    gene_diagnostic_info = load_gene_diagnostic_info(gene_diagnostic_info_file)
+
+    # Load data (Cauchy table and gene diagnostic info)
+    cauchy_table = check_and_run_cauchy_combination(config)
+
+    # Paths to PNGs for gene expression and GSS distribution
+    gss_distribution_dir = config.get_GSS_plot_dir(config.trait_name)
+
+    gene_plots = []
+    plot_select_gene_list = config.get_GSS_plot_select_gene_file(config.trait_name).read_text().splitlines()
+    for gene_name in plot_select_gene_list:
+        expression_png = gss_distribution_dir / f"{config.sample_name}_{gene_name}_Expression_Distribution.png"
+        gss_png = gss_distribution_dir / f"{config.sample_name}_{gene_name}_GSS_Distribution.png"
+        # check if expression and GSS plots exist
+        if not os.path.exists(expression_png) or not os.path.exists(gss_png):
+            print(f"Skipping gene {gene_name} as expression or GSS plot is missing.")
+            continue
+        gene_plots.append({
+            'name': gene_name,
+            'expression_plot': expression_png.relative_to(report_dir),  # Path for gene expression plot
+            'gss_plot': gss_png.relative_to(report_dir)  # Path for GSS distribution plot
+        })
+
+    # # Copy PNG files to the report directory
+    # copy_files_to_report_dir(result_dir, report_dir, [gene['expression_plot'] for gene in gene_plots] + [gene['gss_plot'] for gene in gene_plots])
+
+    # Update paths to point to copied images inside the report folder
+    # for gene in gene_plots:
+    #     gene['expression_plot'] = os.path.join(os.path.basename(gene['expression_plot']))
+    #     gene['gss_plot'] = os.path.join(os.path.basename(gene['gss_plot']))
+
+    # Sample data for other report components
+    title = f"{config.sample_name} Genetic Spatial Mapping Report"
+
+    genetic_mapping_plot = embed_html_content(config.get_gsMap_html_plot_save_path(config.trait_name))
+    manhattan_plot = embed_html_content(config.get_manhattan_html_plot_path(config.trait_name))
+
+    gsmap_version = gsMap.__version__
+    # Render the template with dynamic content, including the run parameters
+
+    trait_name = config.trait_name
+    default_run_parameters = {
+        "Sample Name": config.sample_name,
+        "Trait Name": trait_name,
+        "Summary Statistics File": config.sumstats_file,
+        "HDF5 Path": config.hdf5_with_latent_path,
+        "Annotation": config.annotation,
+        "Spatial LDSC Save Directory": config.ldsc_save_dir,
+        "Cauchy Directory": config.cauchy_save_dir,
+        "Report Directory": config.get_report_dir(trait_name),
+        "gsMap Report File": config.get_gsMap_report_file(trait_name),
+        "Gene Diagnostic Info File": config.get_gene_diagnostic_info_save_path(trait_name),
+        "Report Generation Date": pd.Timestamp.now().strftime('%Y-%m-%d %H:%M:%S'),
+    }
+
+    if run_parameters is not None:
+        default_run_parameters.update(run_parameters)
+
+
+    output_html = template.render(
+        title=title,
+        genetic_mapping_plot=genetic_mapping_plot,  # Inlined genetic mapping plot
+        manhattan_plot=manhattan_plot,  # Inlined Manhattan plot
+        cauchy_table=cauchy_table,
+        gene_plots=gene_plots,  # List of PNG paths for gene plots
+        gsmap_version=gsmap_version,
+        parameters=default_run_parameters,  # Pass the run parameters to the template
+        gene_diagnostic_info=gene_diagnostic_info  # Include top 50 gene diagnostic info rows
+    )
+
+    # Save the generated HTML report in the 'report' directory
+    report_file = config.get_gsMap_report_file(config.trait_name)
+    with open(report_file, "w") as f:
+        f.write(output_html)
+
+    logger.info(f"Report generated successfully! Saved at {report_file}.")
+    logger.info(f"Copy the report directory to your local PC and open the HTML report file in a web browser to view the report.")