adding a umd example to the readme and updating the validation functi…

…on slightly
TeselaGen · Jun 9, 2021 · 849b802 · 849b802
1 parent ce59fbf
commit 849b802
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Showing 3 changed files with 77 additions and 4 deletions.
diff --git a/README.md b/README.md
@@ -97,6 +97,45 @@ or
 
 `yarn add bio-parsers`
 
+or 
+
+use it from a script tag: 
+```html
+<script src="https://unpkg.com/bio-parsers/umd/bio-parsers.js"></script>
+<script>
+      async function main() {
+        var jsonOutput = await window.bioParsers.genbankToJson(
+          `LOCUS       kc2         108 bp    DNA     linear    01-NOV-2016
+COMMENT             teselagen_unique_id: 581929a7bc6d3e00ac7394e8
+FEATURES             Location/Qualifiers
+     CDS             1..108
+                     /label="GFPuv"
+     misc_feature    61..108
+                     /label="gly_ser_linker"
+     bogus_dude      4..60
+                     /label="ccmN_sig_pep"
+     misc_feature    4..60
+                     /label="ccmN_nterm_sig_pep"
+                     /pragma="Teselagen_Part"
+                     /preferred5PrimeOverhangs=""
+                     /preferred3PrimeOverhangs=""
+ORIGIN      
+        1 atgaaggtct acggcaagga acagtttttg cggatgcgcc agagcatgtt ccccgatcgc
+       61 ggtggcagtg gtagcgggag ctcgggtggc tcaggctctg ggg
+//`
+        );
+        console.log('jsonOutput:', jsonOutput);
+        var genbankString = window.bioParsers.jsonToGenbank(jsonOutput[0].parsedSequence);
+        console.log(genbankString);
+      }
+      main();
+</script>
+```
+
+
+
+see the `./umd_demo.html` file for a full working example
+
 ### jsonToGenbank (same interface as jsonToFasta)
 ```js
 //To go from json to genbank:

diff --git a/src/parsers/utils/validateSequence.js b/src/parsers/utils/validateSequence.js
@@ -164,15 +164,14 @@ export default function validateSequence(sequence, options = {}) {
       !areNonNegativeIntegers([feature.end]) ||
       feature.end > sequence.size - (inclusive1BasedEnd ? 0 : 1)
     ) {
+      feature.end = Math.max(sequence.size - 1, inclusive1BasedEnd ? 0 : 1);
       response.messages.push(
         "Invalid feature end:  " +
           feature.end +
           " detected for " +
           feature.name +
-          " and set to 1"
-      ); //setting it to 0 internally, but users will see it as 1
-      feature.end = Math.max(sequence.size - 1, inclusive1BasedEnd ? 0 : 1);
-      // feature.end = 0;
+          " and set to " + (feature.end + 1)
+      );
     }
 
     if (

diff --git a/umd_demo.html b/umd_demo.html
@@ -0,0 +1,35 @@
+<html>
+  <head>
+    <script src="https://unpkg.com/bio-parsers/umd/bio-parsers.js"></script>
+    <!-- you can also specify a version: <script src="https://unpkg.com/bio-parsers@8.3.11/umd/bio-parsers.js"></script> -->
+    <script>
+      async function main() {
+        var jsonOutput = await window.bioParsers.genbankToJson(
+          `LOCUS       kc2         108 bp    DNA     linear    01-NOV-2016
+COMMENT             teselagen_unique_id: 581929a7bc6d3e00ac7394e8
+FEATURES             Location/Qualifiers
+     CDS             1..108
+                     /label="GFPuv"
+     misc_feature    61..108
+                     /label="gly_ser_linker"
+     bogus_dude      4..60
+                     /label="ccmN_sig_pep"
+     misc_feature    4..60
+                     /label="ccmN_nterm_sig_pep"
+                     /pragma="Teselagen_Part"
+                     /preferred5PrimeOverhangs=""
+                     /preferred3PrimeOverhangs=""
+ORIGIN      
+        1 atgaaggtct acggcaagga acagtttttg cggatgcgcc agagcatgtt ccccgatcgc
+       61 ggtggcagtg gtagcgggag ctcgggtggc tcaggctctg ggg
+//`
+        );
+        console.log('jsonOutput:', jsonOutput);
+
+        var genbankString = window.bioParsers.jsonToGenbank(jsonOutput[0].parsedSequence);
+        console.log(genbankString);
+      }
+      main();
+    </script>
+  </head>
+</html>