Translating a DNA to a Protein using server-side javascript and C: my notebook
In my previous post , I used Node.js to translate a DNA to a protein on the Server-side, using javascript. In the following post, I again will translate a DNAn but this time by calling a specialized C program on the server side.
Source code
The C program
The C program reads a DNA string from stdin a translate it using the standard genetic code:
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| #include <stdio.h> | |
| #include <ctype.h> | |
| static const char* STD_GENETIC_CODE="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"; | |
| static int base2index(int 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; | |
| } | |
| }; | |
| static char translate(int b1,int b2,int b3) | |
| { | |
| int base1= base2index(b1); | |
| int base2= base2index(b2); | |
| int base3= base2index(b3); | |
| if(base1==-1 || base2==-1 || base3==-1) | |
| { | |
| return '?'; | |
| } | |
| else | |
| { | |
| return STD_GENETIC_CODE[base1*16+base2*4+base3]; | |
| } | |
| } | |
| static int next_base(FILE* in) | |
| { | |
| int c; | |
| while((c=fgetc(in))!=EOF) | |
| { | |
| if(isspace(c)) continue; | |
| break; | |
| } | |
| return c; | |
| } | |
| int main(void) | |
| { | |
| while(!feof(stdin)) | |
| { | |
| int b1=next_base(stdin); | |
| if(b1==EOF) break; | |
| int b2=next_base(stdin); | |
| if(b2==EOF) break; | |
| int b3=next_base(stdin); | |
| if(b3==EOF) break; | |
| fputc( | |
| translate(b1,b2,b3), | |
| stdout); | |
| } | |
| return 0; | |
| } |
Compilation:
gcc -o /my/bin/path/translate translate.c
The Node.js script
When the Node.js server receive a DNA parameter, it spawns a new process to the C program and we write the DNA to this process via 'stdin'.Each time a new 'data' event (containing the protein) is received, it is printed to the http response. At the end of the process, we close the stream by calling 'end()'.
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| /** | |
| * Author: | |
| * Pierre Lindenbaum | |
| * Mail: | |
| * plindenbaum@yahoo.fr | |
| * WWW: | |
| * http://plindenbaum.blogspot.com | |
| * Motivation: | |
| * Node.js script . translate a DNA to a protein using an external C program | |
| * Usage: | |
| * ${nodejs.dir}/node translate.js | |
| */ | |
| var spawn = require('child_process').spawn | |
| var sys = require('sys'); | |
| querystring = require('querystring'); | |
| function TranslateDna(req,res) | |
| { | |
| if(req.method == 'GET') | |
| { | |
| var params = require('url').parse(req.url,true); | |
| if(params && params.query && params.query.dna) | |
| { | |
| res.writeHead(200, {'Content-type': 'text/plain'}); | |
| var child = spawn('/path/to/bin/translate',[]); | |
| child.stdin.write(params.query.dna); | |
| child.stdout.on('data', function (data) { | |
| res.write(data); | |
| }); | |
| child.stderr.on('data', function (data) { | |
| console.log("stderr:"+data); | |
| }); | |
| child.on('exit', function (data) | |
| { | |
| res.end(); | |
| }); | |
| child.stdin.end(); | |
| return; | |
| } | |
| } | |
| res.writeHead(200, {'Content-type': 'text/html'}); | |
| res.end( | |
| '<html><body><form action="/" method=\"GET\">'+ | |
| '<h1>DNA</h1>'+ | |
| '<textarea name="dna"></textarea><br/>' + | |
| '<input type="submit" value="Submit">' + | |
| '</form></body></html>' | |
| ); | |
| } | |
| http = require('http'); | |
| var nodeserver = http.createServer(TranslateDna); | |
| nodeserver.listen(8080); | |
| console.log('Server running at http://127.0.0.1:8080/'); | |
test
> node-v0.2.5/node translate.js
Server running at http://127.0.0.1:8080
> curl -s "http://localhost:8080/?dna=ATGATGATAGATAGATATAGTAGATATGATCGTCAGCCATACG"
MMIDRYSRYDRQPY
Server running at http://127.0.0.1:8080
> curl -s "http://localhost:8080/?dna=ATGATGATAGATAGATATAGTAGATATGATCGTCAGCCATACG"
MMIDRYSRYDRQPY
That's it,
Pierre
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