Major refactor of the database generation tool

.codacy.yml

@@ -0,0 +1,5 @@
+---
+exclude_paths:
+  - "docs/stylesheets/**"
+  - "docs/plans/**"
+  - "pgatk/tests/**"

.github/workflows/deploy-docs.yml

@@ -0,0 +1,43 @@
+name: Deploy Documentation
+
+on:
+  push:
+    branches: ["master"]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  deploy-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Cache pip dependencies
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-mkdocs
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install MkDocs and dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install mkdocs-material
+
+      - name: Build MkDocs documentation
+        run: |
+          mkdocs build --strict
+
+      - name: Deploy to GitHub Pages
+        run: |
+          mkdocs gh-deploy --force --message "docs: deploy documentation [skip ci]"

.github/workflows/pythonapp.yml

@@ -46,7 +46,7 @@ jobs:
     - name: Test with unittest
       shell: bash -l {0}
       run: |
-        cd pypgatk
+        cd pgatk
         python -m unittest discover -s tests -p "*_tests.py" -v
 
     - name: Update changelog
@@ -67,7 +67,7 @@ jobs:
       shell: bash -l {0}
       run: |
         pip install pytest pytest-cov coverage
-        cd pypgatk
+        cd pgatk
         coverage run -m unittest discover -s tests -p "*_tests.py"
         coverage xml -o coverage.xml
 

.github/workflows/pythonpackage.yml

@@ -46,5 +46,5 @@ jobs:
     - name: Test with unittest
       shell: bash -l {0}
       run: |
-        cd pypgatk
+        cd pgatk
         python -m unittest discover -s tests -p "*_tests.py" -v

.gitignore

@@ -108,17 +108,30 @@ venv.bak/
 .pydevproject
 
 .idea/
-pypgatk/database_ensembl/
-pypgatk/database_cbioportal/
-pypgatk/database_cosmic/
-pypgatk/config/private/
+pgatk/database_ensembl/
+pgatk/database_cbioportal/
+pgatk/database_cosmic/
+pgatk/config/private/
 .pypirc
-/pypgatk/test_all.bed
-/pypgatk/test_annotated.vcf
-
+/pgatk/test_all.bed
+/pgatk/test_annotated.vcf
+
+# Test-generated output files (produced by pgatk tests)
+pgatk/testdata/proteindb_from_*.fa
+pgatk/testdata/output_decoy.fa
+pgatk/testdata/test_cbioportal_data_mutations_mskcc_proteindb*.fa
+pgatk/testdata/test_cosmic_mutations_proteindb*.fa
+pgatk/testdata/test_blast_psms_out.tsv
+pgatk/testdata/test_blast_validate_psms_out.tsv
+pgatk/testdata/test_validate_psms_out.tsv
+pgatk/testdata/20151020_QE3_UPLC8_DBJ_SA_HCT116_Rep2_46frac_10_consensus_filter.idxml
+pgatk/testdata/proteindb_minus_strand_test.fa
+
+# Large Ensembl reference files (download at test time, not in git)
+pgatk/testdata/Meleagris_gallopavo*
 
 #Ignore cursor AI rules
 .cursor/rules/codacy.mdc
 .DS_Store
 .codacy/
-.cursor/
+.cursor/

CHANGELOG.md

@@ -1,96 +1,96 @@
 # Changelog
 
-## [v0.0.24](https://github.com/bigbio/py-pgatk/tree/v0.0.24) (2024-04-19)
+## [v0.0.24](https://github.com/bigbio/pgatk/tree/v0.0.24) (2024-04-19)
 
 **Implemented enhancements:**
 
-- change var\_prefix [\#66](https://github.com/bigbio/py-pgatk/issues/66)
+- change var\_prefix [\#66](https://github.com/bigbio/pgatk/issues/66)
 
-## [v0.0.23](https://github.com/bigbio/py-pgatk/tree/v0.0.23) (2022-07-07)
+## [v0.0.23](https://github.com/bigbio/pgatk/tree/v0.0.23) (2022-07-07)
 
-## [v0.0.22](https://github.com/bigbio/py-pgatk/tree/v0.0.22) (2022-06-21)
+## [v0.0.22](https://github.com/bigbio/pgatk/tree/v0.0.22) (2022-06-21)
 
-## [v0.0.21](https://github.com/bigbio/py-pgatk/tree/v0.0.21) (2022-06-17)
+## [v0.0.21](https://github.com/bigbio/pgatk/tree/v0.0.21) (2022-06-17)
 
 **Implemented enhancements:**
 
-- gffread fasta generated file uses space and semicolon [\#59](https://github.com/bigbio/py-pgatk/issues/59)
+- gffread fasta generated file uses space and semicolon [\#59](https://github.com/bigbio/pgatk/issues/59)
 
 **Fixed bugs:**
 
-- Write urls for download into file instead of downloading  [\#61](https://github.com/bigbio/py-pgatk/issues/61)
-- changing values in the config files have no effect [\#58](https://github.com/bigbio/py-pgatk/issues/58)
+- Write urls for download into file instead of downloading  [\#61](https://github.com/bigbio/pgatk/issues/61)
+- changing values in the config files have no effect [\#58](https://github.com/bigbio/pgatk/issues/58)
 
-## [v0.0.20](https://github.com/bigbio/py-pgatk/tree/v0.0.20) (2022-05-10)
+## [v0.0.20](https://github.com/bigbio/pgatk/tree/v0.0.20) (2022-05-10)
 
 **Implemented enhancements:**
 
-- Implementation of Class FDR [\#56](https://github.com/bigbio/py-pgatk/issues/56)
-- Cleaning the code [\#50](https://github.com/bigbio/py-pgatk/issues/50)
+- Implementation of Class FDR [\#56](https://github.com/bigbio/pgatk/issues/56)
+- Cleaning the code [\#50](https://github.com/bigbio/pgatk/issues/50)
 
 **Fixed bugs:**
 
-- pyVCF reader deprecated only supported for py3.6  [\#55](https://github.com/bigbio/py-pgatk/issues/55)
+- pyVCF reader deprecated only supported for py3.6  [\#55](https://github.com/bigbio/pgatk/issues/55)
 
 **Closed issues:**
 
-- Fasta input for vcf-to-proteindb [\#29](https://github.com/bigbio/py-pgatk/issues/29)
+- Fasta input for vcf-to-proteindb [\#29](https://github.com/bigbio/pgatk/issues/29)
 
-## [v0.0.19](https://github.com/bigbio/py-pgatk/tree/v0.0.19) (2021-03-31)
+## [v0.0.19](https://github.com/bigbio/pgatk/tree/v0.0.19) (2021-03-31)
 
-## [v0.0.18](https://github.com/bigbio/py-pgatk/tree/v0.0.18) (2021-03-30)
+## [v0.0.18](https://github.com/bigbio/pgatk/tree/v0.0.18) (2021-03-30)
 
 **Fixed bugs:**
 
-- Downloading all the cBioPortal experiments failing  [\#20](https://github.com/bigbio/py-pgatk/issues/20)
+- Downloading all the cBioPortal experiments failing  [\#20](https://github.com/bigbio/pgatk/issues/20)
 
-## [v0.0.17](https://github.com/bigbio/py-pgatk/tree/v0.0.17) (2021-03-12)
+## [v0.0.17](https://github.com/bigbio/pgatk/tree/v0.0.17) (2021-03-12)
 
-## [v0.0.16](https://github.com/bigbio/py-pgatk/tree/v0.0.16) (2021-03-06)
+## [v0.0.16](https://github.com/bigbio/pgatk/tree/v0.0.16) (2021-03-06)
 
-## [v0.0.15](https://github.com/bigbio/py-pgatk/tree/v0.0.15) (2021-02-17)
+## [v0.0.15](https://github.com/bigbio/pgatk/tree/v0.0.15) (2021-02-17)
 
-## [v0.0.14](https://github.com/bigbio/py-pgatk/tree/v0.0.14) (2021-02-15)
+## [v0.0.14](https://github.com/bigbio/pgatk/tree/v0.0.14) (2021-02-15)
 
-## [v0.0.13](https://github.com/bigbio/py-pgatk/tree/v0.0.13) (2021-02-15)
+## [v0.0.13](https://github.com/bigbio/pgatk/tree/v0.0.13) (2021-02-15)
 
-## [v0.0.12](https://github.com/bigbio/py-pgatk/tree/v0.0.12) (2021-02-11)
+## [v0.0.12](https://github.com/bigbio/pgatk/tree/v0.0.12) (2021-02-11)
 
-## [v0.0.11](https://github.com/bigbio/py-pgatk/tree/v0.0.11) (2021-02-07)
+## [v0.0.11](https://github.com/bigbio/pgatk/tree/v0.0.11) (2021-02-07)
 
-## [v0.0.10](https://github.com/bigbio/py-pgatk/tree/v0.0.10) (2021-02-05)
+## [v0.0.10](https://github.com/bigbio/pgatk/tree/v0.0.10) (2021-02-05)
 
 **Implemented enhancements:**
 
-- Ensembl release [\#23](https://github.com/bigbio/py-pgatk/issues/23)
-- Add a changelog.md to the project  [\#22](https://github.com/bigbio/py-pgatk/issues/22)
+- Ensembl release [\#23](https://github.com/bigbio/pgatk/issues/23)
+- Add a changelog.md to the project  [\#22](https://github.com/bigbio/pgatk/issues/22)
 
-## [v0.0.9](https://github.com/bigbio/py-pgatk/tree/v0.0.9) (2021-02-03)
+## [v0.0.9](https://github.com/bigbio/pgatk/tree/v0.0.9) (2021-02-03)
 
 **Implemented enhancements:**
 
-- overlap between config parameters in cgenomes between cosmic and cbioportal downloaders [\#17](https://github.com/bigbio/py-pgatk/issues/17)
-- Major review to the code [\#8](https://github.com/bigbio/py-pgatk/issues/8)
+- overlap between config parameters in cgenomes between cosmic and cbioportal downloaders [\#17](https://github.com/bigbio/pgatk/issues/17)
+- Major review to the code [\#8](https://github.com/bigbio/pgatk/issues/8)
 
 **Fixed bugs:**
 
-- Error from ENSEMBL URL retry  [\#25](https://github.com/bigbio/py-pgatk/issues/25)
+- Error from ENSEMBL URL retry  [\#25](https://github.com/bigbio/pgatk/issues/25)
 
-## [v0.0.8](https://github.com/bigbio/py-pgatk/tree/v0.0.8) (2021-01-19)
+## [v0.0.8](https://github.com/bigbio/pgatk/tree/v0.0.8) (2021-01-19)
 
 **Implemented enhancements:**
 
-- Cosmic mutations for celllines  [\#28](https://github.com/bigbio/py-pgatk/issues/28)
+- Cosmic mutations for celllines  [\#28](https://github.com/bigbio/pgatk/issues/28)
 
-## [v0.0.7](https://github.com/bigbio/py-pgatk/tree/v0.0.7) (2021-01-11)
+## [v0.0.7](https://github.com/bigbio/pgatk/tree/v0.0.7) (2021-01-11)
 
-## [v0.0.6](https://github.com/bigbio/py-pgatk/tree/v0.0.6) (2020-05-02)
+## [v0.0.6](https://github.com/bigbio/pgatk/tree/v0.0.6) (2020-05-02)
 
 **Implemented enhancements:**
 
-- Add the decoy Sanger tool to the library  [\#19](https://github.com/bigbio/py-pgatk/issues/19)
-- Major refactoring of the library to be more package oriented design [\#13](https://github.com/bigbio/py-pgatk/issues/13)
-- Create / Download Canonical protein fasta file from ENSEMBL  [\#1](https://github.com/bigbio/py-pgatk/issues/1)
+- Add the decoy Sanger tool to the library  [\#19](https://github.com/bigbio/pgatk/issues/19)
+- Major refactoring of the library to be more package oriented design [\#13](https://github.com/bigbio/pgatk/issues/13)
+- Create / Download Canonical protein fasta file from ENSEMBL  [\#1](https://github.com/bigbio/pgatk/issues/1)
 
 
 

Dockerfile

@@ -1,7 +1,7 @@
 FROM biocontainers/biocontainers:debian-stretch-backports
 MAINTAINER Yasset Perez-Riverol <ypriverol@gmail.com>
-LABEL software="pypgatk" \
-    container="pypgatk" \
+LABEL software="pgatk" \
+    container="pgatk" \
     software.version="0.0.26" \
     version="1"
 
@@ -13,11 +13,9 @@ WORKDIR /data
 RUN mkdir -p /tool/source
 
 RUN git config --global http.sslVerify false
-RUN git clone --depth 1 https://github.com/bigbio/py-pgatk.git /tool/source
+RUN git clone --depth 1 https://github.com/bigbio/pgatk.git /tool/source
 WORKDIR /tool/source
 RUN pip3 install --no-cache-dir -r requirements.txt && pip3 install --no-cache-dir -e .
 
 ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
-ENV PATH=$PATH:/tool/source/pypgatk/
-RUN chmod +x /tool/source/pypgatk/pypgatkc.py

MANIFEST.in

@@ -1,5 +1,5 @@
  include *.md
  include *.txt
  include *.yaml
- recursive-include pypgatk *.json
- recursive-include pypgatk *.yaml
+ recursive-include pgatk *.json
+ recursive-include pgatk *.yaml