Merge pull request #81 from mpi2/scripts

Write script to access `Applied method` field in old releases in `scripts` folder with helper scripts

scripts/count_method.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# In[ ]:
+
+
+"""This script processes a ZIP file to count occurrences
+of applied methods within output_Successful.tsv files in Results_IMPC_SP_Windowed.zip.
+The script is executed from the command line with the path to the ZIP file as an argument. 
+The results are outputted in separate JSON files for each pattern, summarizing the counts
+of the applied methods found in the processed files."""
+
+import json
+import re
+import sys
+import zipfile
+from collections import Counter
+
+def count_method(input_zip):
+    # Initialize counters
+    counters = {p: Counter() for p in ("_IPG_010_001", "_IPG_011_001", "_IPG_012_001")}
+
+    # Open the ZIP file
+    with zipfile.ZipFile(input_zip, 'r') as zip_file:
+        # Iterate through each file in the ZIP
+        for file_info in zip_file.infolist():
+            # Get the file name
+            file_name = file_info.filename
+            # Check all patterns
+            for pattern, counter in counters.items():
+                # Check if the pattern matches the file name and if the file name is "output_Successful.tsv"
+                if re.search(pattern, file_name) and file_name.endswith("output_Successful.tsv"):
+                    # Extract file content
+                    with zip_file.open(file_name) as file:
+                        file_content = file.read().decode('utf-8')
+                        json_string = file_content.split('\t')[-1]
+                        # Convert JSON string to Python dictionary
+                        stats_results = json.loads(json_string)
+                        # Extract the value of "Applied method"
+                        applied_method = stats_results["Result"]["Vector output"]["Normal result"]["Applied method"]
+                        # Update the counter
+                        counter.update([applied_method])
+
+    # Write counters to separate files
+    for param, counter in counters.items():
+        with open("".join([param[-11:], ".json"]), 'w') as f:
+            json.dump(counter, f, indent=4)
+
+if __name__ == "__main__":
+    import argparse
+    parser = argparse.ArgumentParser(description="Process zip file and count applied methods.")
+    parser.add_argument("zip_file", help="Path to the zip file")
+    args = parser.parse_args()
+    count_method(args.zip_file)
+

eye_patch.py → scripts/eye_patch.py

@@ -1,4 +1,4 @@
-"""This is a temporary module to synchronise the parameters/options lists with IMPRESS.
+"""This is a temporary module to synchronise the parameters/options lists with IMPReSS.
 Given the size of the files (CategoryRemapping.tsv, MergeParameterList.txt), it's impossible
 to modify them by hand, so this module is used instead. In the future, parameter mapping
 and representation will be improved and refactored, so this module will no longer be necessary."""