Merge pull request #68 from Clinical-Genomics/master

Merging clinical genomics fork

.bumpversion.cfg

@@ -0,0 +1,8 @@
+[bumpversion]
+current_version = 2.1.8
+commit = True
+tag = True
+tag_name = {new_version}
+message = Bump version: {current_version} -> {new_version} [skip ci]
+
+[bumpversion:file:fusion_report/__init__.py]

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,3 +9,9 @@ Thank you for contribution to `fusion-report` project.
 - [ ] Documentation in `docs` is updated
 - [ ] `CHANGELOG.md` is updated
 - [ ] `README` is updated
+
+### This [version](https://semver.org/) is a
+
+- [ ] **MAJOR** - when you make incompatible API changes
+- [ ] **MINOR** - when you add functionality in a backwards compatible manner
+- [ ] **PATCH** - when you make backwards compatible bug fixes or documentation/instructions

.github/workflows/bump_version.yml

@@ -0,0 +1,17 @@
+name: "Bump Version"
+on:
+ push:
+ branches:
+ - "master"
+jobs:
+ bump-version:
+ runs-on: ubuntu-latest
+ name: Bump version and push tags to master
+ steps:
+ - name: Bump version
+ uses: Clinical-Genomics/bump2version-ci@v3
+ env:
+ BUMPVERSION_TOKEN: ${{ secrets.BUMPVERSION_TOKEN }}
+ BUMPVERSION_AUTHOR: ${{ secrets.BUMPVERSION_AUTHOR }}
+ BUMPVERSION_EMAIL: ${{ secrets.BUMPVERSION_EMAIL }}
+ GITHUB_REPOSITORY: ${{ github.repository }}

.github/workflows/integration_tests.yml

@@ -0,0 +1,33 @@
+name: Integration Tests
+
+on:
+ pull_request:
+ branches: [master]
+
+jobs:
+ build:
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.8
+ uses: actions/setup-python@v1
+ with:
+ python-version: 3.8
+
+ - name: Install dependencies & package
+ run: |
+ python -m pip install --upgrade pip
+ pip install -r requirements.txt -r requirements-dev.txt
+ python setup.py install
+
+ - name: Test download of databases
+ run: fusion_report download --cosmic_usr "${{ secrets.COSMIC_USERNAME }}" --cosmic_passwd "${{ secrets.COSMIC_PASSWD }}" ./db
+
+ - name: Test run
+ run: |
+ fusion_report run "example-sample" ./docs/example ./db/ \
+ --arriba tests/test_data/arriba.tsv \
+ --fusioncatcher tests/test_data/fusioncatcher.txt \
+ --starfusion tests/test_data/starfusion.tsv \
+ --export csv

.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Black
+
+on: [pull_request]
+
+jobs:
+ lint:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out git repository
+ uses: actions/checkout@v3
+
+ - name: Setup Python 3.8
+ uses: actions/setup-python@v4
+ with:
+ python-version: 3.8
+
+ - name: Set up Black
+ uses: psf/black@stable
+ with:
+ options: ". --check --line-length 100"
+ version: "~=23.3.0"

.github/workflows/publish_image.yml

@@ -0,0 +1,32 @@
+name: Build and publish image on new release event
+
+on:
+ release:
+ types:
+ - created
+
+jobs:
+ docker-image-release_push:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check Out Repo
+ uses: actions/checkout@v3
+
+ - name: Login to Docker Hub
+ uses: docker/login-action@v2
+ with:
+ username: ${{ secrets.DOCKER_USERNAME }}
+ password: ${{ secrets.DOCKER_PASSWORD }}
+
+ - name: Set up Docker Buildx
+ id: buildx
+ uses: docker/setup-buildx-action@v2
+
+ - name: Build and push
+ id: docker_build
+ uses: docker/build-push-action@v3
+ with:
+ context: ./
+ file: ./Dockerfile
+ push: true
+ tags: "clinicalgenomics/fusion-report:${{github.event.release.tag_name}}"

.gitignore

@@ -12,3 +12,5 @@ tests/sss
 *.log
 .tox/
 .DS_Store
+testfusionreport.sh
+thisismydb/

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.1.8]
+
+### Removed
+
+- Removed FusionGDB
+
 ## [2.1.5](https://github.com/matq007/fusion-report/releases/tag/2.1.5)
 
 ### Added

README.md

@@ -40,7 +40,7 @@ python3 setup.py install
 
 ```bash
 # Download required databases
-# Currently supported databases: FusionGDB, Mitelman and COSMIC
+# Currently supported databases: FusionGDB2, Mitelman and COSMIC
 # COSMIC requires login credentials to download Fusion gene Database
 fusion_report download --cosmic_usr '<username>' --cosmic_passwd '<password>' /path/to/db/
 

docs/add_database.md

@@ -31,7 +31,7 @@ class Test(Db, metaclass=Singleton):
 
 ```python
 local_fusions: Dict[str, List[str]] = {
- FusionGDB(path).name: FusionGDB(path).get_all_fusions(),
+ FusionGDB2(path).name: FusionGDB2(path).get_all_fusions(),
  MitelmanDB(path).name: MitelmanDB(path).get_all_fusions(),
  CosmicDB(path).name: CosmicDB(path).get_all_fusions(),
  TestDB(path).name: TestDB(path).get_all_fusions() # add your database here

docs/download.md

@@ -2,7 +2,7 @@
 
 Currently the tool supports three different databases:
 
-* [FusionGDB](https://ccsm.uth.edu/FusionGDB/index.html)
+* [FusionGDB2](https://compbio.uth.edu/FusionGDB2/tables)
 * [Mitelman](https://cgap.nci.nih.gov/Chromosomes/Mitelman)
 * [COSMIC](https://cancer.sanger.ac.uk/cosmic/fusion)
 
@@ -15,24 +15,19 @@ fusion_report download
  /path/to/db
 ```
 
-## Manual download
-
-### FusionGDB
-
-Website: [https://ccsm.uth.edu/FusionGDB/index.html](https://ccsm.uth.edu/FusionGDB/index.html)
+With a non-academic/research login -> using QIAGEN with a commercial license:
 
 ```bash
-# Download all files
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/TCGA_ChiTaRS_combined_fusion_information_on_hg19.txt -O TCGA_ChiTaRS_combined_fusion_information_on_hg19.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt -O TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/uniprot_gsymbol.txt -O uniprot_gsymbol.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/fusion_uniprot_related_drugs.txt -O fusion_uniprot_related_drugs.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/fusion_ppi.txt -O fusion_ppi.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/fgene_disease_associations.txt -O fgene_disease_associations.txt
-# Create database and import the data
-sqlite3 fusiongdb.db < fusion_report/db/FusionGDB.sql
+fusion_report download
+ --cosmic_usr '<QIAGEN username>'
+ --cosmic_passwd 'QIAGEN <password>'
+ --qiagen
+ /path/to/db
 ```
 
+
+## Manual download
+
 ### Mitelman
 
 Website: [https://cgap.nci.nih.gov/Chromosomes/Mitelman](https://cgap.nci.nih.gov/Chromosomes/Mitelman)

docs/score.md

@@ -4,17 +4,16 @@ One disadvantage of the tools is that they tend to report false positive results
 estimated score for a fusion. The only way how to correctly verify a fusion is biologically (RT-qPCR …).
 
 **fusion-report** uses weighted approach of assigning weights to tools and databases. By default, each tool
-is assigned the same weight. This is because each tool uses different approach of discovering fusions and 
+is assigned the same weight. This is because each tool uses different approach of discovering fusions and
 report different results, for example FusionCatcher will work best on somatic samples.
 
 You can customize weight of individual tool by specific parameter `<tool-name>_weight 30`.
 The sum of the weights has to be 100!
 
 Currently weights for databases are not adjustable. The weights for databases are as follows:
 
-* FusionGDB (20)
-* COSMIC (40)
-* MITELMAN (40)
+* COSMIC (50)
+* MITELMAN (50)
 * FusionGDB2 (0)
 
 > It is strongly suggested to use all supported databases in order to get the best estimated score.

fusion_report/__init__.py

@@ -0,0 +1,2 @@
+__title__ = "fusion_report"
+__version__ = "2.1.8"