Merge pull request #8 from chrovis/feature/signature-db-loader

Add signature database loader with COSMIC style

.github/workflows/format.yml

@@ -0,0 +1,26 @@
+name: format
+
+on: [push, pull_request]
+
+jobs:
+  format:
+    runs-on: ubuntu-18.04
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup Java
+      uses: actions/setup-java@v3
+      with:
+        java-version: '11'
+        distribution: 'adopt'
+        architecture: x64
+    - name: Cache m2 repository
+      uses: actions/cache@v3
+      with:
+        path: ~/.m2
+        key: ${{ runner.os }}-m2-${{ hashFiles('**/project.clj') }}
+        restore-keys: |
+          ${{ runner.os }}-m2-
+    - name: Install dependencies
+      run: lein deps
+    - name: Run cljfmt
+      run: lein cljfmt check

.github/workflows/lint.yml

@@ -0,0 +1,20 @@
+name: lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name : master base sha
+      id : master_base_sha
+      if : github.ref  == 'refs/heads/master'
+      run: echo  "::set-output name=base_sha::${{ github.event.before }}"
+    - uses: xcoo/[email protected]
+      with:
+        linters: "[\"clj-kondo\" \"kibit\" \"eastwood\"]"
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        runner: ":leiningen"
+        base_sha: ${{ github.event.pull_request.base.sha||steps.master_base_sha.outputs.base_sha }}
+        eastwood_linters: "[:all]"

.github/workflows/main.yml

@@ -0,0 +1,37 @@
+name: main
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: [ '8', '11', '16', '17']
+        clojure: [ '1.9', '1.10', '1.11' ]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup Java
+      uses: actions/setup-java@v3
+      with:
+        java-version: ${{ matrix.java }}
+        distribution: 'adopt'
+        architecture: x64
+    - name: Setup Node.js
+      uses: actions/setup-node@v3
+      with:
+        node-version: latest
+    - name: Cache m2 repository
+      uses: actions/cache@v3
+      with:
+        path: ~/.m2
+        key: ${{ runner.os }}-m2-${{ hashFiles('**/project.clj') }}
+        restore-keys: |
+          ${{ runner.os }}-m2-
+    - name: Install dependencies
+      run: |
+        lein deps
+    - name: Run tests
+      run: |
+        lein with-profile +dev:+${{ matrix.clojure }} test
+        lein with-profile +dev,+${{ matrix.clojure }} doo node test once

README.md

@@ -4,13 +4,13 @@
 
 # clj-deconstruct-sigs
 
-![Mutational Signature](https://cancer.sanger.ac.uk/signatures/Signature-1.png "Mutational Signature")
+![Mutational Signature](docs/img/v3.2_SBS3_PROFILE_GA_GRCh37_ygeJJyb.original.jpg "Mutational Signature")
 
 clj-deconstruct-sigs is a Clojure port of [deconstructSigs](https://github.com/raerose01/deconstructSigs).
 
 ## What are Mutational Signatures?
 
-A comprehensive description can be found [here](https://cancer.sanger.ac.uk/cosmic/signatures).
+You can find a comprehensive description [here](https://cancer.sanger.ac.uk/cosmic/signatures).
 In short, treating an individual's somatic mutation pattern as a combination of known distinct signatures could lead to insights of cancer's characteristics.
 
 ## Usage
@@ -19,15 +19,15 @@ The main function is `clj-deconstruct-sigs.core/which-signatures`, which takes a
 
 ```
 :seed-idx - Index of the signature that was used as the initial seed
-:weights  - A map of weight indices to weight. :weights* with zero contribution entries
-:weights* - A map of non-zero weight indices to weight. Note that entries that have zero contribution will be missing.
+:weights  - A map of weight indices to weight.
+:weights-with-names  - A map of weight that associated signature names as key on behalf of indices.
 :product - matrix product of :weights and the provided signatures
 :unknown - 1 minus the sum of weights
 :diff - element wise difference of the provided sample tumor and the product
 :error-sum - Square root of the sum of the element wise square of :diff. Indicates how close the :product is from the original input
 ```
 
-Here is a repl session that adds more context.
+Here is a REPL session that adds more context.
 
 ```clojure
 (require '[clj-deconstruct-sigs.core :refer :all])
@@ -39,13 +39,14 @@ Here is a repl session that adds more context.
 ;; Reference set of signatures to use, represented with m rows x 96 columns.
 ;; This library provides cosmic.signature-data.generated/latest-cosmic-signatures which is based on parsing the latest
 ;; signatures at https://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt
-(require '[clj-deconstruct-sigs.data.cosmic])
+(require '[clj-deconstruct-sigs.db])
+(def cosmic-signatures (clj-deconstruct-sigs.db/load-signature-database "dev-resources/COSMIC_v3.2_SBS_GRCh38.txt"))
 
-(which-signatures sample-tumor clj-deconstruct-sigs.data.cosmic/cosmic-signatures)
+(which-signatures sample-tumor cosmic-signatures)
 =>
 {:seed-idx 25,
- :weights {7 0.36016636298023036,...},
- :weights* {0 0.0, ...},
+ :weights {0 0.36016636298023036,...},
+ :weights-with-names {"SBS1" 0.36016636298023036,...},
  :product [6.690145741717268E-4,...],
  :unknown 0.09329024976612943,
  :diff [6.451870662289333E-4,...],
@@ -54,6 +55,6 @@ Here is a repl session that adds more context.
 
 ## License
 
-Copyright 2019 [Xcoo, Inc.](https://xcoo.jp/)
+Copyright 2019-2022 [Xcoo, Inc.](https://xcoo.jp/)
 
 Licensed under the [Apache License, Version 2.0](LICENSE).