From 8704f3ad2d156e5d6956899039f3a06e20337bb8 Mon Sep 17 00:00:00 2001 From: jaeyeon Date: Tue, 18 Nov 2025 13:16:17 -0600 Subject: [PATCH 1/4] hotfix --- bin/location_to_gene.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From f7418bbcee09b775dc9941a4bc2ad084a3b1a68f Mon Sep 17 00:00:00 2001 From: jaeyeon Date: Mon, 15 Dec 2025 16:01:11 -0600 Subject: [PATCH 2/4] bump up to 1.1.3 --- README.md | 2 +- docs/source/conf.py | 2 +- nextflow.config | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 38d35f7..ff8c8d0 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@

- + Documentation Status 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/nextflow.config b/nextflow.config index 64e9aa5..eba02ac 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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' From baf60659f36daba4a7f01446e978119551719de2 Mon Sep 17 00:00:00 2001 From: jaeyeon Date: Tue, 16 Dec 2025 09:26:34 -0600 Subject: [PATCH 3/4] Use and instruct aim data dependencies 2.4 public as default --- README.md | 2 +- docs/source/installation.rst | 2 +- nextflow.config | 2 +- nextflow_schema.json | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index ff8c8d0..4ff45b2 100644 --- a/README.md +++ b/README.md @@ -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/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 eba02ac..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 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 From bc7c17079492c497efdac843d6884e02e29d76d7 Mon Sep 17 00:00:00 2001 From: jaeyeon Date: Thu, 18 Dec 2025 09:51:20 -0600 Subject: [PATCH 4/4] Fix a bug that NA value can be in phrank --- bin/generate_new_matrix_2.py | 1 + 1 file changed, 1 insertion(+) 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")