diff --git a/README.md b/README.md index 38d35f7..4ff45b2 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@
-
+
@@ -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
diff --git a/bin/generate_new_matrix_2.py b/bin/generate_new_matrix_2.py
index 783cf52..c667b0b 100755
--- a/bin/generate_new_matrix_2.py
+++ b/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")
diff --git a/bin/location_to_gene.py b/bin/location_to_gene.py
index b7dec00..6c412ec 100755
--- a/bin/location_to_gene.py
+++ b/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
diff --git a/docs/source/conf.py b/docs/source/conf.py
index a624939..b3408bd 100644
--- a/docs/source/conf.py
+++ b/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 ---------------------------------------------------
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index 6d9b1f9..7d68f76 100644
--- a/docs/source/installation.rst
+++ b/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::
diff --git a/nextflow.config b/nextflow.config
index 64e9aa5..e92c799 100644
--- a/nextflow.config
+++ b/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'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c01c3b5..1a319d7 100644
--- a/nextflow_schema.json
+++ b/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