Fix loading of crispresso info from WGS and Pooled

pinellolab · Jul 20, 2022 · 49740ba · 49740ba
1 parent b68a432
commit 49740ba
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Showing 3 changed files with 13 additions and 5 deletions.
diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py
@@ -420,9 +420,7 @@ def main():
         can_finish_incomplete_run = False
         if args.no_rerun:
             if os.path.exists(crispresso2_info_file):
-                previous_run_data = CRISPRessoShared.load_crispresso_info(
-                    OUTPUT_DIRECTORY,
-                )
+                previous_run_data = CRISPRessoShared.load_crispresso_info(crispresso_info_file_path=crispresso2_info_file)
                 if previous_run_data['running_info']['version'] == CRISPRessoShared.__version__:
                     args_are_same = True
                     for arg in vars(args):

diff --git a/CRISPResso2/CRISPRessoShared.py b/CRISPResso2/CRISPRessoShared.py
@@ -554,13 +554,21 @@ def object_hook(self, obj):
 def load_crispresso_info(
     crispresso_output_folder="",
     crispresso_info_file_name='CRISPResso2_info.json',
+    crispresso_info_file_path=None
 ):
     """Load the CRISPResso2 info for a CRISPResso run.
 
+        If crispresso_info_file_path is given, attempt to read info file at that location
+        Otherwise, read file at crispresso_output_folder/crispresso_info_file_name
+
     Parameters
     ----------
     crispresso_output_folder : string
         Path to CRISPResso folder
+    crispresso_info_file_name : string
+        Name of info file in CRISPResso folder
+    crispresso_info_path: string
+        Path to info file
 
     Returns
     -------
@@ -571,6 +579,9 @@ def load_crispresso_info(
     crispresso_info_file = os.path.join(
         crispresso_output_folder, crispresso_info_file_name,
     )
+    if crispresso_info_file_path is not None:
+        crispresso_info_file = crispresso_info_file_path
+
     if not os.path.isfile(crispresso_info_file):
         raise Exception('Cannot open CRISPResso info file at ' + crispresso_info_file)
     try:

diff --git a/CRISPResso2/CRISPRessoWGSCORE.py b/CRISPResso2/CRISPRessoWGSCORE.py
@@ -6,7 +6,6 @@
 '''
 
 
-import argparse
 from datetime import datetime
 import gzip
 import os
@@ -381,7 +380,7 @@ def print_stacktrace_if_debug():
         can_finish_incomplete_run = False
         if args.no_rerun:
             if os.path.exists(crispresso2_info_file):
-                previous_run_data = CRISPRessoShared.load_crispresso_info(OUTPUT_DIRECTORY)
+                previous_run_data = CRISPRessoShared.load_crispresso_info(crispresso_info_file_path=crispresso2_info_file)
                 if previous_run_data['running_info']['version'] == CRISPRessoShared.__version__:
                     args_are_same = True
                     for arg in vars(args):