Created
April 22, 2011 20:29
-
-
Save lindenb/937535 to your computer and use it in GitHub Desktop.
Translate a DNA to protein using HTML5+ File API.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <html> | |
| <head> | |
| </head> | |
| <body> | |
| <form> | |
| <label for="ZmlsZXMKfiles">Select a FASTA file</label>:<input type="file" id="ZmlsZXMKfiles" multiple="true"/> | |
| </form> | |
| <script type="application/ecmascript"> | |
| var GENETIC_CODE="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"; | |
| function base2index(c) | |
| { | |
| switch(c) | |
| { | |
| case 'T':case 't': return 0; | |
| case 'C':case 'c': return 1; | |
| case 'A':case 'a': return 2; | |
| case 'G':case 'g': return 3; | |
| default: return -1; | |
| } | |
| } | |
| function translate(dna) | |
| { | |
| var prot=""; | |
| for(var i=0;i+2 < dna.length;i+=3) | |
| { | |
| var base1= base2index(dna[i+0]); | |
| var base2= base2index(dna[i+1]); | |
| var base3= base2index(dna[i+2]); | |
| if(base1==-1 || base2==-1 || base3==-1) | |
| { | |
| prot+='?'; | |
| } | |
| else | |
| { | |
| prot+=GENETIC_CODE[base1*16+base2*4+base3]; | |
| } | |
| } | |
| return prot; | |
| } | |
| function readingFasta(evt) | |
| { | |
| if (!evt.lengthComputable) return; | |
| var loaded = (evt.loaded / evt.total); | |
| if (loaded > 1) return; | |
| var pre=document.getElementById('ZmlsZXMKtext'); | |
| while(pre.hasChildNodes()) pre.removeChild( pre.firstChild ); | |
| pre.appendChild(document.createTextNode("Reading "+Math.round(loaded*100)+"%")); | |
| } | |
| function endReadFasta(e) | |
| { | |
| var pre=document.getElementById('ZmlsZXMKtext'); | |
| while(pre.hasChildNodes()) pre.removeChild( pre.firstChild ); | |
| var lines=e.target.result.split("\n"); | |
| var dna=""; | |
| var i=0; | |
| var line; | |
| for(;;) | |
| { | |
| if(i==lines.length || (line=lines[i].replace(/^\s+|\s+$/g,""))[0]=='>') | |
| { | |
| if(dna.length > 0) | |
| { | |
| var prot=translate(dna); | |
| var j=0; | |
| while(j < prot.length) | |
| { | |
| pre.appendChild(document.createTextNode(prot.substring(j,j+50))); | |
| pre.appendChild(document.createElement("br")); | |
| j+=50; | |
| } | |
| } | |
| if(i===lines.length) break; | |
| pre.appendChild(document.createTextNode(line)); | |
| pre.appendChild(document.createElement("br")); | |
| dna=""; | |
| } | |
| else | |
| { | |
| dna+=line; | |
| } | |
| ++i; | |
| } | |
| } | |
| function handleFileSelect(evt) | |
| { | |
| var files = evt.target.files; // FileList object | |
| if(files.length!=1) return; | |
| var reader = new FileReader(); | |
| reader.onprogress=readingFasta; | |
| reader.onloadend=endReadFasta; | |
| var pre=document.getElementById('ZmlsZXMKtext'); | |
| while(pre.hasChildNodes()) pre.removeChild( pre.firstChild ); | |
| pre.appendChild(document.createTextNode("Reading "+files[0].name+"...")); | |
| reader.readAsText(files[0]); | |
| } | |
| document.getElementById('ZmlsZXMKfiles').addEventListener('change', handleFileSelect, false); | |
| </script> | |
| <pre id="ZmlsZXMKtext"></pre> | |
| </body> | |
| </html> |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment