diff --git a/README.md b/README.md index 38d35f7..4ff45b2 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@

- + 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 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