Hotfix: v1.1.3

README.md

@@ -7,7 +7,7 @@
 
 <p align="center">
   <a style="text-decoration:none">
-    <img src="https://img.shields.io/badge/AI_MARRVEL-v1.1.2-blue.svg"/>
+    <img src="https://img.shields.io/badge/AI_MARRVEL-v1.1.3-blue.svg"/>
   </a>
   <a href='https://ai-marrvel.readthedocs.io/en/latest/?badge=latest'>
     <img src='https://readthedocs.org/projects/ai-marrvel/badge/?version=latest' alt='Documentation Status' />
@@ -37,7 +37,7 @@ AIM utilizes various databases for variant annotation, all of which have been co
    ```
 3. Use the following command to sync the S3 bucket to your local directory:
    ```bash
-   $ aws s3 sync s3://aim-data-dependencies-2.3-public . --no-sign-request
+   $ aws s3 sync s3://aim-data-dependencies-2.4-public . --no-sign-request
    ```
 
 ### Get the software

bin/generate_new_matrix_2.py

@@ -19,6 +19,7 @@ def main():
 
     ### get original coordinates ###
     merged["varId"] = merged["varId"].apply(lambda x: x.split("_E")[0])
+    merged["varId"] = merged["varId"].apply(lambda x: x.split("_-")[0])
 
     phr = pd.read_csv(path_phrank, sep="\t", names=["ENSG", "phrank"])
     merged = merged.merge(phr, left_on="geneEnsId", right_on="ENSG", how="left")

bin/location_to_gene.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python
 import sys
 import os
 from collections import defaultdict

docs/source/conf.py

@@ -21,7 +21,7 @@
 # The short X.Y version
 version = 'v1.1'
 # The full version, including alpha/beta/rc tags
-release = '1.1.2'
+release = '1.1.3'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/installation.rst

@@ -61,7 +61,7 @@ AIM utilizes various databases for variant annotation, all of which have been co
 
 .. code-block:: bash
 
-      aws s3 sync s3://aim-data-dependencies-2.3-public . --no-sign-request
+      aws s3 sync s3://aim-data-dependencies-2.4-public . --no-sign-request
 
 
 .. warning::

nextflow.config

@@ -10,7 +10,7 @@ params {
     run_id = "run1"
     ref_ver = "hg19"
     ref_dir = null
-    s3_bucket_data_name = "aim-data-dependencies-2.3-public"
+    s3_bucket_data_name = "aim-data-dependencies-2.4-public"
     bed_filter = null
     exome_filter = false
     impact_filter = false
@@ -42,7 +42,7 @@ profiles {
 manifest {
     author          = 'LiuzLab'
     name            = 'LiuzLab/AI_MARRVEL'
-    version         = '1.1.2'
+    version         = '1.1.3'
 
     description     = """AI-MARRVEL (AIM) is an AI system for rare genetic disease diagnosis."""
     homePage        = 'https://github.com/LiuzLab/AI_MARRVEL'

nextflow_schema.json

@@ -55,7 +55,7 @@
         },
         "s3_bucket_data_name": {
           "type": "string",
-          "default": "aim-data-dependencies-2.3-public",
+          "default": "aim-data-dependencies-2.4-public",
           "description": "[Not Implemented] S3 bucket name to aim pipeline dependencies directory.",
           "format": "path",
           "hidden": true