tg-seq-gen 1.0.6 → 1.0.8

package/helperFns.js

@@ -4,6 +4,57 @@ const defaultCount = 10;
 const defaultMaxLength = 10000;
 const defaultMinLength = 1000;
 
+// Feature types that can appear in GenBank files
+const featureTypes = [
+  "CDS",
+  "gene",
+  "misc_feature",
+  "promoter",
+  "terminator",
+  "rep_origin",
+  "enhancer",
+  "attenuator",
+  "misc_binding",
+  "protein_bind",
+  "misc_signal",
+  "regulatory",
+];
+
+// Function to generate a random feature for GenBank format
+function generateRandomFeature(seqLength) {
+  // Select a random feature type
+  const featureType =
+    featureTypes[Math.floor(Math.random() * featureTypes.length)];
+
+  // Generate a random start position (at least 10bp from the end)
+  const maxStart = Math.max(1, seqLength - 10);
+  const start = Math.floor(Math.random() * maxStart) + 1;
+
+  // Generate a random end position (between start and end of sequence)
+  const end = Math.floor(Math.random() * (seqLength - start)) + start;
+
+  // Generate a random name for the feature
+  const featureName = `feature_${Math.floor(Math.random() * 10000)}`;
+
+  // Format the feature in GenBank style
+  return `     ${featureType}             ${start}..${end}
+                     /label="${featureName}"
+                     /note="randomly generated feature"
+`;
+}
+
+// Function to generate multiple random features for a sequence
+function generateFeatures(seqLength, numFeatures) {
+  let features = "";
+  if (numFeatures > 0) {
+    features = "FEATURES             Location/Qualifiers\n";
+    for (let i = 0; i < numFeatures; i++) {
+      features += generateRandomFeature(seqLength);
+    }
+  }
+  return features;
+}
+
 function genHelper(
   {
     count = defaultCount,
@@ -83,12 +134,24 @@ function getBps({ length, maxLength, minLength, isCDS }) {
 function getSequenceFileForType(opts) {
   if (opts.type === "gb") {
     return genHelper(opts, ({ name, bps }) => {
+      // Get the current date in the format used in GenBank files
+      const today = new Date();
+      const dateString = today.toLocaleDateString('en-US', {
+        day: '2-digit',
+        month: 'short',
+        year: 'numeric'
+      }).replace(/(\w+)-(\d+)-(\d+)/, '$1-$3').toUpperCase();
+      
+      // Generate features if numFeatures is specified
+      const features = opts.numFeatures ? generateFeatures(bps.length, opts.numFeatures) : '';
+      
       return (
         "LOCUS       " +
         name +
         "         " +
         bps.length +
-        " bp    DNA     linear  19-NOV-2018\n" +
+        " bp    DNA     linear  " + dateString + "\n" +
+        features +
         "ORIGIN      \n" +
         "        1 " +
         bps +
@@ -113,7 +176,7 @@ function getSequenceFileForType(opts) {
       }
     );
   } else if (opts.type === "fasta") {
-    genHelper(opts, ({ name, bps }) => {
+    return genHelper(opts, ({ name, bps }) => {
       return ">" + name + "||" + bps.length + "|linear\n" + bps;
     });
   }

package/index.js

@@ -13,7 +13,7 @@ const {
 } = require("./helperFns");
 
 program
-  .version("1.0.3")
+  .version("1.0.7")
   .description(
     "Generate sequences of varying formats (gb|csv|fasta). By default it will generate 100 sequences with random lengths between 1k and 10k bps"
   )
@@ -37,6 +37,11 @@ program
     defaultCount
   )
   .option("-t, --type [type]", "choose one of [gb|csv|fasta]", "gb")
+  .option(
+    "-f, --numFeatures [numFeatures]",
+    "number of random features to add to genbank files",
+    0
+  )
   .parse(process.argv);
 
 console.info("file type: ", program.type);

package/package.json

@@ -1,11 +1,12 @@
 {
   "name": "tg-seq-gen",
-  "version": "1.0.6",
+  "version": "1.0.8",
   "description": "dna sequence generator",
   "main": "index.js",
   "repository": "https://github.com/TeselaGen/tg-seq-gen",
   "scripts": {
-    "test": "node test.js"
+    "test": "node index.test.js",
+    "test:shell": "bash shell-test.sh"
   },
   "author": "Teselagen",
   "license": "MIT",

package/shell-test.sh

@@ -0,0 +1,96 @@
+#!/bin/bash
+# Simple shell test script for tg-seq-gen
+
+# Define test status
+TEST_SUCCESS=0
+TEST_FAILURE=0
+
+# Helper function for checking test results
+check_test() {
+  if [ $? -eq 0 ]; then
+    echo -e "\033[32m✓ $1\033[0m"
+    ((TEST_SUCCESS++))
+  else
+    echo -e "\033[31m✗ $1\033[0m"
+    ((TEST_FAILURE++))
+  fi
+}
+
+# Helper function to run a command with proper error handling
+run_test() {
+  local cmd="$1"
+  local description="$2"
+  
+  echo "Running: $cmd"
+  if eval "$cmd" > /dev/null 2>&1; then
+    check_test "$description"
+    return 0
+  else
+    check_test "$description"
+    return 1
+  fi
+}
+
+# Make sure we're in the correct directory
+cd "$(dirname "$0")" || exit 1
+
+# Define the command - use local index.js directly for testing
+CMD="node ./index.js"
+
+echo "Running shell tests for tg-seq-gen..."
+echo "======================================"
+
+# Test 1: Check if node is available
+command -v node >/dev/null 2>&1
+check_test "Node.js is available"
+
+# Test 2: Check if the script exists
+[ -f "./index.js" ]
+check_test "index.js exists"
+
+# Test 3: Generate default GenBank file
+$CMD -t gb -c 1
+check_test "Generate default GenBank file"
+[ -f "pTG_001.gb" ] && rm "pTG_001.gb"
+
+# Test 4: Generate default FASTA file
+$CMD -t fasta -c 1
+check_test "Generate default FASTA file"
+[ -f "pTG_001.fasta" ] && rm "pTG_001.fasta"
+
+# Test 5: Generate CSV file
+$CMD -t csv -c 1
+check_test "Generate default CSV file"
+[ -f "pTG_001.csv" ] && rm "pTG_001.csv"
+
+# Test 6: Generate with custom lengths
+$CMD -t gb -c 1 -l 500,600
+check_test "Generate GenBank with custom lengths"
+[ -f "pTG_001.gb" ] && rm "pTG_001.gb"
+
+# Test 7: Generate with min/max length parameters
+$CMD -t fasta -c 1 -i 200 -m 500
+check_test "Generate FASTA with min/max length"
+[ -f "pTG_001.fasta" ] && rm "pTG_001.fasta"
+
+# Test 8: Generate GenBank with features
+$CMD -t gb -c 1 -f 5
+check_test "Generate GenBank with features"
+[ -f "pTG_001.gb" ] && rm "pTG_001.gb"
+
+# Test 9: Check help output
+$CMD --help | grep -q "Generate sequences"
+check_test "Help command works properly"
+
+# Test 10: Check version output
+$CMD --version | grep -q "1.0.7"
+check_test "Version command works properly"
+
+# Print test summary
+echo "======================================"
+echo "Tests completed: $((TEST_SUCCESS + TEST_FAILURE))"
+echo "Tests passed: $TEST_SUCCESS"
+echo "Tests failed: $TEST_FAILURE"
+
+# Return exit code based on test results
+[ "$TEST_FAILURE" -eq 0 ] && exit 0 || exit 1