clustal-js - npm Package Compare versions

Comparing version 1.0.4 to 2.0.0

CHANGELOG.md

@@ -0,1 +1,9 @@
+# v2.0.0
+
+- Parse pairwise format, outputted by e.g. EMBOSS needle, etc
+
+# v1.0.4
+
+- Fix package name in README
+
 # v1.0.3
@@ -5,3 +13,2 @@
 
-
 ## v1.0.2
@@ -8,0 +15,0 @@

package.json

 {
   "name": "clustal-js",
-  "version": "1.0.4",
+  "version": "2.0.0",
   "main": "dist/index.js",
@@ -11,24 +11,14 @@ "repository": "cmdcolin/clustal-js",
   "devDependencies": {
-    "@babel/cli": "^7.12.10",
-    "@babel/core": "^7.12.10",
-    "@babel/plugin-proposal-class-properties": "^7.12.1",
-    "@babel/plugin-transform-runtime": "^7.12.10",
-    "@babel/preset-env": "^7.12.11",
-    "@babel/preset-typescript": "^7.12.7",
-    "@types/jest": "^26.0.20",
-    "@types/node": "^14.14.22",
-    "@typescript-eslint/eslint-plugin": "^4.14.2",
-    "@typescript-eslint/parser": "^4.14.2",
-    "babel-eslint": "^10.0.1",
-    "babel-jest": "^26.6.3",
-    "eslint": "^7.19.0",
-    "eslint-config-airbnb-base": "^14.2.1",
-    "eslint-config-prettier": "^7.2.0",
-    "eslint-plugin-import": "^2.22.1",
-    "eslint-plugin-prettier": "^3.3.1",
-    "jest": "^26.6.3",
-    "jest-cli": "^26.6.3",
-    "prettier": "^2.2.1",
-    "ts-jest": "^26.5.0",
-    "typescript": "^4.1.3"
+    "@types/jest": "^29.5.12",
+    "@types/node": "^20.11.16",
+    "@typescript-eslint/eslint-plugin": "^6.21.0",
+    "@typescript-eslint/parser": "^6.21.0",
+    "eslint": "^8.56.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^50.0.1",
+    "jest": "^29.7.0",
+    "prettier": "^3.2.5",
+    "ts-jest": "^29.1.2",
+    "typescript": "^5.3.3"
   },
@@ -35,0 +25,0 @@ "scripts": {

README.md

@@ -7,7 +7,6 @@ [![Build Status](https://travis-ci.com/cmdcolin/clustal-js.svg?branch=master)](https://travis-ci.com/cmdcolin/clustal-js)
 
-
 ## Usage
 
-```js
-import {parse} from 'clustal-js'
+```typescript
+import { parse } from 'clustal-js'
 const file = fs.readFileSync('test.aln', 'utf8')
@@ -61,5 +60,102 @@ const ret = parse(file)
 
+### Parse pairwise outputs
 
+```typescript
+import { parsePairwise } from 'clustal-js'
+const file = fs.readFileSync('test.aln', 'utf8')
+const ret = parse(file)
+```
+
+Input test.aln (e.g. from EMBOSS needle)
+
+```
+########################################
+# Program: needle
+# Rundate: Mon  5 Feb 2024 17:52:19
+# Commandline: needle
+#    -auto
+#    -stdout
+#    -asequence emboss_needle-R20240205-175207-0261-70863964-p1m.asequence
+#    -bsequence emboss_needle-R20240205-175207-0261-70863964-p1m.bsequence
+# Align_format: srspair
+# Report_file: stdout
+########################################
+
+#=======================================
+#
+# Aligned_sequences: 2
+# 1: a
+# 2: b
+# Matrix: EBLOSUM62
+# Gap_penalty: 10.0
+# Extend_penalty: 0.5
+#
+# Length: 614
+# Identity:     221/614 (36.0%)
+# Similarity:   221/614 (36.0%)
+# Gaps:         393/614 (64.0%)
+# Score: 1114.0
+#
+#
+#=======================================
+
+a                  1 MGQKGHKDSLYPCGGTPESSLHEALDQCMTALDLFLTNQFSEALSYLKPR     50
+
+b                  0 --------------------------------------------------      0
+
+a                 51 TKESMYHSLTYATILEMQAMMTFDPQDILLAGNMMKEAQMLCQRHRRKSS    100
+
+b                  0 --------------------------------------------------      0
+
+a                101 VTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQRAALTFLQGSSHGGAV    150
+
+b                  0 --------------------------------------------------      0
+
+a                151 RPRALHDPSHACSCPPGPGRQHLFLLQDENMVSFIKGGIKVRNSYQTYKE    200
+
+b                  0 --------------------------------------------------      0
+
+a                201 LDSLVQSSQYCKGENHPHFEGGVKLGVGAFNLTLSMLPTRILRLLEFVGF    250
+
+b                  0 --------------------------------------------------      0
+
+a                251 SGNKDYGLLQLEEGASGHSFRSVLCVMLLLCYHTFLTFVLGTGNVNIEEA    300
+
+b                  0 --------------------------------------------------      0
+
+a                301 EKLLKPYLNRYPKGAIFLFFAGRIEVIKGNIDAAIRRFEECCEAQQHWKQ    350
+
+b                  0 --------------------------------------------------      0
+
+a                351 FHHMCYWELMWCFTYKGQWKMSYFYADLLSKENCWSKATYIYMKAAYLSM    400
+                                                               ||||||||
+b                  1 ------------------------------------------MKAAYLSM      8
+
+a                401 FGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNP    450
+                     ||||||||||||||||||||||||||||||||||||||||||||||||||
+b                  9 FGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNP     58
+
+a                451 ISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIITKAEEMLEKGPENEYS    500
+                     ||||||||||||||||||||||||||||||||||||||||||||||||||
+b                 59 ISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIITKAEEMLEKGPENEYS    108
+
+a                501 VDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALL    550
+                     ||||||||||||||||||||||||||||||||||||||||||||||||||
+b                109 VDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALL    158
+
+a                551 ELALLLMEQDRNEEAIKLLESAKQNYKNYSMESRTHFRIQAATLQAKSSL    600
+                     ||||||||||||||||||||||||||||||||||||||||||||||||||
+b                159 ELALLLMEQDRNEEAIKLLESAKQNYKNYSMESRTHFRIQAATLQAKSSL    208
+
+a                601 ENSSRSMVSSVSL-    613
+                     |||||||||||||
+b                209 ENSSRSMVSSVSL*    222
+
+
+#---------------------------------------
+#---------------------------------------
+```
+
 ### Notes
 
 See tests for example files

No alert changes

Improved metrics

Total package byte prevSize

6791

increased by85.45%

Dev dependency count

12

decreased by-45.45%

Number of lines in readme file

160

increased by150%

No dependency changes