clustal-js 1.0.4 → 2.0.0

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Files changed (3) hide show
  1. package/CHANGELOG.md +8 -1
  2. package/README.md +99 -3
  3. package/package.json +13 -23
package/CHANGELOG.md CHANGED
@@ -1,8 +1,15 @@
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+ # v2.0.0
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+
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+ - Parse pairwise format, outputted by e.g. EMBOSS needle, etc
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+
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+ # v1.0.4
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+
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+ - Fix package name in README
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+
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  # v1.0.3
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  - Add generated typescript declarations to output
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-
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  ## v1.0.2
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  - Add dist folder to package.json
package/README.md CHANGED
@@ -4,11 +4,10 @@
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  This parses clustal output format
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-
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  ## Usage
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- ```js
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- import {parse} from 'clustal-js'
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+ ```typescript
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+ import { parse } from 'clustal-js'
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  const file = fs.readFileSync('test.aln', 'utf8')
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  const ret = parse(file)
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  ```
@@ -57,6 +56,103 @@ Output
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  version: '1.2.4' } }
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  ```
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+ ### Parse pairwise outputs
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+
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+ ```typescript
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+ import { parsePairwise } from 'clustal-js'
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+ const file = fs.readFileSync('test.aln', 'utf8')
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+ const ret = parse(file)
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+ ```
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+
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+ Input test.aln (e.g. from EMBOSS needle)
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+
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+ ```
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+ ########################################
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+ # Program: needle
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+ # Rundate: Mon 5 Feb 2024 17:52:19
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+ # Commandline: needle
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+ # -auto
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+ # -stdout
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+ # -asequence emboss_needle-R20240205-175207-0261-70863964-p1m.asequence
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+ # -bsequence emboss_needle-R20240205-175207-0261-70863964-p1m.bsequence
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+ # Align_format: srspair
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+ # Report_file: stdout
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+ ########################################
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+
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+ #=======================================
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+ #
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+ # Aligned_sequences: 2
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+ # 1: a
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+ # 2: b
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+ # Matrix: EBLOSUM62
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+ # Gap_penalty: 10.0
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+ # Extend_penalty: 0.5
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+ #
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+ # Length: 614
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+ # Identity: 221/614 (36.0%)
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+ # Similarity: 221/614 (36.0%)
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+ # Gaps: 393/614 (64.0%)
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+ # Score: 1114.0
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+ #
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+ #
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+ #=======================================
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+
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+ a 1 MGQKGHKDSLYPCGGTPESSLHEALDQCMTALDLFLTNQFSEALSYLKPR 50
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+
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+ b 0 -------------------------------------------------- 0
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+ a 51 TKESMYHSLTYATILEMQAMMTFDPQDILLAGNMMKEAQMLCQRHRRKSS 100
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+ b 0 -------------------------------------------------- 0
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+
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+ a 101 VTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQRAALTFLQGSSHGGAV 150
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+ b 0 -------------------------------------------------- 0
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+ a 151 RPRALHDPSHACSCPPGPGRQHLFLLQDENMVSFIKGGIKVRNSYQTYKE 200
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+ b 0 -------------------------------------------------- 0
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+
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+ a 201 LDSLVQSSQYCKGENHPHFEGGVKLGVGAFNLTLSMLPTRILRLLEFVGF 250
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+ b 0 -------------------------------------------------- 0
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+
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+ a 251 SGNKDYGLLQLEEGASGHSFRSVLCVMLLLCYHTFLTFVLGTGNVNIEEA 300
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+ b 0 -------------------------------------------------- 0
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+ a 301 EKLLKPYLNRYPKGAIFLFFAGRIEVIKGNIDAAIRRFEECCEAQQHWKQ 350
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+ b 0 -------------------------------------------------- 0
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+ a 351 FHHMCYWELMWCFTYKGQWKMSYFYADLLSKENCWSKATYIYMKAAYLSM 400
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+ ||||||||
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+ b 1 ------------------------------------------MKAAYLSM 8
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+
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+ a 401 FGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNP 450
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||
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+ b 9 FGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNP 58
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+
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+ a 451 ISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIITKAEEMLEKGPENEYS 500
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||
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+ b 59 ISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIITKAEEMLEKGPENEYS 108
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+
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+ a 501 VDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALL 550
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||
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+ b 109 VDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALL 158
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+
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+ a 551 ELALLLMEQDRNEEAIKLLESAKQNYKNYSMESRTHFRIQAATLQAKSSL 600
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||
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+ b 159 ELALLLMEQDRNEEAIKLLESAKQNYKNYSMESRTHFRIQAATLQAKSSL 208
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+
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+ a 601 ENSSRSMVSSVSL- 613
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+ |||||||||||||
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+ b 209 ENSSRSMVSSVSL* 222
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+
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+
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+ #---------------------------------------
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+ #---------------------------------------
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+ ```
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  ### Notes
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package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "clustal-js",
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- "version": "1.0.4",
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+ "version": "2.0.0",
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  "main": "dist/index.js",
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  "repository": "cmdcolin/clustal-js",
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  "files": [
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  ],
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  "license": "MIT",
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  "devDependencies": {
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- "@babel/cli": "^7.12.10",
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- "@babel/core": "^7.12.10",
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- "@babel/plugin-proposal-class-properties": "^7.12.1",
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- "@babel/plugin-transform-runtime": "^7.12.10",
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- "@babel/preset-env": "^7.12.11",
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- "@babel/preset-typescript": "^7.12.7",
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- "@types/jest": "^26.0.20",
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- "@types/node": "^14.14.22",
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- "@typescript-eslint/eslint-plugin": "^4.14.2",
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- "@typescript-eslint/parser": "^4.14.2",
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- "babel-eslint": "^10.0.1",
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- "babel-jest": "^26.6.3",
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- "eslint": "^7.19.0",
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- "eslint-config-airbnb-base": "^14.2.1",
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- "eslint-config-prettier": "^7.2.0",
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- "eslint-plugin-import": "^2.22.1",
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- "eslint-plugin-prettier": "^3.3.1",
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- "jest": "^26.6.3",
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- "jest-cli": "^26.6.3",
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- "prettier": "^2.2.1",
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- "ts-jest": "^26.5.0",
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- "typescript": "^4.1.3"
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+ "@types/jest": "^29.5.12",
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+ "@types/node": "^20.11.16",
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+ "@typescript-eslint/eslint-plugin": "^6.21.0",
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+ "@typescript-eslint/parser": "^6.21.0",
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+ "eslint": "^8.56.0",
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+ "eslint-config-prettier": "^9.1.0",
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+ "eslint-plugin-prettier": "^5.1.3",
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+ "eslint-plugin-unicorn": "^50.0.1",
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+ "jest": "^29.7.0",
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+ "prettier": "^3.2.5",
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+ "ts-jest": "^29.1.2",
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+ "typescript": "^5.3.3"
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  },
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  "scripts": {
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  "test": "jest",