Metaxcan erros issue template

.github/ISSUE_TEMPLATE/metaxcan-errors.md

@@ -0,0 +1,27 @@
+---
+name: Metaxcan errors
+about: Use this template to raise an issue on error related to MetaXcan software family
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+# Instant help
+Search your error message on the [FAQ](https://predictdb.org/categories/faq/) for instant help. If you can't find it proceed with the next steps below.
+
+# System info
+- Operating system : [Mac, Linux, Windows]
+- OS version:   
+- Did you install and use this [conda env](https://github.com/hakyimlab/MetaXcan/blob/master/software/conda_env.yaml)?
+
+# Error info
+- Paste the specific command you used
+
+- Rerun the command and set `--verbosity 7` and paste the error log here
+
+- Headers of your input files
+
+- Genome build of your input files
+
+- Any other important info

software/Predict.py

@@ -161,6 +161,10 @@ def run(args):
 
     logging.info("Loading model")
     model, weights, extra = model_structure(args)
+
+    if args.shuffle_weights:
+        logging.info("Shuffling weights in model")
+        weights["weight"] = weights.groupby("gene")["weight"].transform(numpy.random.permutation)
 
     variant_mapping = get_variant_mapping(args, weights)
 
@@ -256,6 +260,7 @@ def add_arguments(parser):
     parser.add_argument("--sub_batch", help="compute on a specific slice of data", type=int, default=None)
     parser.add_argument("--only_entries", help="Compute only these entries in the models (e.g. a whitelist of genes)", nargs="+")
     parser.add_argument("--capture")
+    parser.add_argument('--shuffle_weights', action="store_true", help="shuffle model weights to check for inflation")
 
 if __name__ == "__main__":
     import argparse

software/SPrediXcan.py

@@ -56,6 +56,7 @@ def run(args):
     parser.add_argument("--overwrite", help="If set, will overwrite the results file if it exists.", action="store_true", default=False)
     parser.add_argument("--additional_output", help="If set, will output additional information.", action="store_true", default=False)
     parser.add_argument("--MAX_R", help="Run only for the first R genes", type=int, default=None)
+    parser.add_argument('--shuffle_weights', action="store_true", help="shuffle model weights to check for inflation")
 
     args = parser.parse_args()
 

software/metax/metaxcan/Utilities.py

@@ -250,6 +250,10 @@ def build_context(args, gwas):
     logging.info("Loading model from: %s", args.model_db_path)
     model = load_model(args.model_db_path, args.model_db_snp_key)
 
+    if args.shuffle_weights:
+        logging.info("Shuffling weights in model")
+        model.weights["weight"] = model.weights.groupby("gene")["weight"].transform(numpy.random.permutation)
+
     if not args.single_snp_model:
         if not args.stream_covariance:
             logging.info("Loading covariance data from: %s", args.covariance)