motifWeb.js

request = require("request")
var restful="http://127.0.0.1:8081"

function list(sp,callback) {
request(
	{url:restful+"/list"+sp+"h"
		,json:true},
	function(err,res,body) {
		callback(body)
 		}
	)
}
function getAln(gene,callback) {
		request(
		{url:restful+"/bl2seq_r?gene="+gene ,json:true},
		function(err,res,body) {
		   callback(body)
		})
}

function getMotifs(genome,gene,callback) {
		request(
		{url:restful+"/"+genome+"_cp_motifs?gene="+gene ,json:true},
		function(err,res,body) {
		   callback(body)
		})

}
function getAll(gene,callback,callback2) {
	var done=0;
	var hMotifs,mMotifs,Aln;
	getAln(gene,function(d){
		Aln=d;
		if(d.length>0) {
		var human_gene=d[0].subject_id
		getMotifs("hg19",human_gene,function(d){
			hMotifs=d.motifs;
			done+=1;
			if(done==2) {callback({"aln":Aln,"h":hMotifs,"m":mMotifs},callback2)}
        	})
		getMotifs("mm10",gene,
		function(d) {
			mMotifs=d.motifs;
			done+=1;
			if(done==2) {callback({"aln":Aln,"h":hMotifs,"m":mMotifs},callback2)}
	 	}
		)
		} else {
		   callback({"aln":[],"h":[],"m":[]},callback2);
		}
		}
	)
}



function translate(coord_start,coord_end,start,end) {
	if (coord_end>coord_start) {
		return [start-coord_start,end-coord_start]
	} else {
		return [coord_end-end, coord_end-start]
	}

}
function proc(d,callback) {
	g=[];
	if(!d.aln) {callback(g)}
	else {
	d.aln.forEach( function(a) {
	   var m_start = a.q_start
	   var m_end = a.q_end
	   var m_max=Math.max(m_start,m_end)
	   var m_min=Math.min(m_start,m_end)
	   var h_start = a.s_start
	   var h_end = a.s_end
   	   var h_max=Math.max(h_start,h_end)
	   var h_min=Math.min(h_start,h_end)
	 
	   var m_a=[]
	   var h_a=[]
	   d.m.forEach(function(motif) {
		if(motif[2]>m_min && motif[1] < m_max) {
			var x=translate(m_start,m_end,motif[1],motif[2])
			s=x[0]
			e=x[1]
			m_a.push({"name":motif[0],"s":s,"e":e,"motif":motif})
		  }
		})
	   d.h.forEach(function(motif) {
		if(motif[2]>h_min && motif[1] < h_max) {
			var x=translate(h_start,h_end,motif[1],motif[2])
			s=x[0]
			e=x[1]
			h_a.push({"name":motif[0],"s":s,"e":e,"motif":motif})
		  }
		})
	    var cm=[]
	    h_a.forEach(function(h_m) {
		m_a.forEach(function(m_m) {
			if (m_m.name==h_m.name && m_m.s < h_m.e && m_m.e > h_m.s) {
			cm.push([m_m.name,m_m.s,m_m.e,h_m.s,h_m.e])
			}
		})
	    })
	    if(cm.length>1) {g.push(a,cm)}	
	})
	callback(g)
	}
}
function cb(d) {console.log(JSON.stringify(d));}
/*
list("mouse",function(genes) {
	genes.forEach(function(d,i){
	console.log("# ",i,d)
	getAll(d,process);
	})
     })	
*/
module.exports = {
	homoloMotifs : function(gene,callback) {
		g=getAll(gene,proc,callback);
	}

}

restapi.js

var fs = require('fs');
var motifWeb = require("./motifWeb");
function readLines(input, func) {
  var remaining = '';

  input.on('data', function(data) {
    remaining += data;
    var index = remaining.indexOf('\n');
    while (index > -1) {
      var line = remaining.substring(0, index);
      remaining = remaining.substring(index + 1);
      func(line);
      index = remaining.indexOf('\n');
    }
  });

  input.on('end', function() {
    if (remaining.length > 0) {
      func(remaining);
    }
  });
}

var enrichedMotifs={}
function func(data) {
  enrichedMotifs[data]=1;
}

var input = fs.createReadStream('data/enriched.motif.list');
readLines(input, func);


var sqlite3 = require('sqlite3').verbose();
var express = require('express');
var restapi = express();

/***** SECTION FOR mouse tpm ******/
var mouseTpmDb = new sqlite3.Database("data/Mouse_tpm.sqlite3.db")
var mouseTpm={};
mouseTpmDb.each("SELECT * from tbl",function(err,row){
	mouseTpm[row.gene]=row;
})
restapi.get('/mousetpm',function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	var geneids;
	if (typeof req.query.genes==="string") {
		geneids=req.query.genes.split(",");
	} else {
		geneids=req.query.genes;
	}
	var retv=[];
	geneids.forEach(function(geneid){
	if (mouseTpm[geneid]) {
		retv.push(mouseTpm[geneid]);
	  }
	})
	res.json(retv);
	
},function(){
})
/****SECTION FOR HomeGene DB *******/
var homodb = new sqlite3.Database("data/homogene.sqlite3.db")
var m2h={}
var h2m={}
var mouseHomologenes,humanHomologenes;
homodb.each("SELECT Mouse,Human from tbl",function(err,row){
	m2h[row.Mouse]=row.Human;
	h2m[row.Human]=row.Mouse;
},function(){
	mouseHomologenes=Object.keys(m2h)
	humanHomologenes=Object.keys(h2m)
	homodb.close();
});
restapi.get('/m2h',function(req,res) {
	if (req.query.genes) {
	var retv=translate(req.query.genes,m2h);
    	res.setHeader("Access-Control-Allow-Origin", "*");
	res.json(retv)
	} else {
	res.status(500)
	}
		
});
restapi.get('/listmouseh',function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	res.json(mouseHomologenes)	
})

restapi.get('/listhumanh',function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	res.json(humanHomologenes)
})
restapi.get('/h2m',function(req,res) {
	if (req.query.genes) {
	var retv=translate(req.query.genes,h2m);
    	res.setHeader("Access-Control-Allow-Origin", "*");
	res.json(retv)
	} else {
	res.status(500);
	}
		
});

function translate(genes,map) {
	if (typeof genes === "string") {
		genes=genes.split(",")
	}
	var retv={"homogene":[],"unknown":[]};
	genes.forEach(function(d) {
		if (map[d]) {
			retv.homogene.push(map[d])
		}
		else {
			retv.unknown.push(d);
		}
	})
	return retv;

}

/****SECTION FOR:$
 * GeneSet DB *******/
var qs = require('querystring');
var dbs = ["test.db","elisa.db"];
var db={};
dbs.forEach(function(d){
	db[d] = new sqlite3.Database("data/"+d);
db[d].serialize(function() {
    //db.run("CREATE TABLE IF NOT EXISTS geneset (key TEXT, value INTEGER)");
});
})
restapi.get('/list', function(req, res){
    var a=[]
    var d=req.query.db || "test.db"
    res.setHeader("Access-Control-Allow-Origin", "*");
    db[d].each("SELECT id,genesetid,groupid FROM geneset", function(err, row){
	a.push(row);
    },
   function() {
        res.json(a)
      }
    )
});

restapi.get('/data', function(req, res){
    res.setHeader("Access-Control-Allow-Origin", "*");
    var d=req.query.db || "test.db"
   db[d].get("SELECT id,genesetid,groupid,geneset,description FROM geneset where id=?",req.query.id, function(err, row){
	res.json(row);
    }
    )
});



restapi.post('/data', function(req, res){
    	var body=""
    	var d=req.query.db || "test.db"
    	res.setHeader("Access-Control-Allow-Origin", "*");
	req.on("data",function(data) {
		body+=data;
	})
	req.on("end",function() {
	var post = qs.parse(body);
	var geneset = post["geneset[]"].join(",");
	var groupid=post.groupid || "";
	db[d].run("INSERT INTO geneset(genesetid,groupid,geneset,author,description) VALUES (?,?,?,?,?)", [post.genesetid,groupid,geneset,post.author,post.description] , function(err, row){
	if (err){
            res.status(500);
        }
        else {
            res.status(202);
        }
        res.end();
    		})
	})
        
});

/*
restapi.delete('/data', function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	console.log("deleting");
	res.send("aha insight");
})
*/
restapi.get('/delete', function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
    	var d=req.query.db || "test.db"
	db[d].run("DELETE FROM geneset WHERE id=?",req.query.id,function(err){},function(){
		var a={"status":req.query.id+" deleted"}
		res.json(a);
	});
})
restapi.post('/put', function(req, res){
    	var body=""
    	var d=req.query.db || "test.db"
    	res.setHeader("Access-Control-Allow-Origin", "*");
	req.on("data",function(data) {
		body+=data;
	})
	req.on("end",function() {
	var post = qs.parse(body);
	var geneset = post["geneset[]"].join(",");
	var groupid=post.groupid || "";
    db[d].run('update geneset set genesetid=?,groupid=?,description=?,geneset=? where id=?',[post.genesetid,groupid,post.description,geneset,post.id], function(err, row){
	if (err){
            console.err(err);
            res.status(500);
        }
        else {
            res.status(202);
        }
        res.end();
    		})
	})
        
});
/********** SECTION FOR MOTIFS TFS POS *******/

var PosDb = new sqlite3.Database("data/hg19_one_tr_per_gene.motifs.tf.sqlite3.db")
function isEnriched(d) {
	if(enrichedMotifs[d[0]]) {return true}
	else {return false}	
}
restapi.get('/hg19_cp_motifs', function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	PosDb.get("SELECT * FROM tbl WHERE gene=?",req.query.gene,function(err,row){
		if(err) {
            		res.status(500);
		} else {
		var a={};
                if(row) {
		a["gene"]=row.gene
		if (req.query.enriched) {
			a["motifs"]=JSON.parse(row.motifs.replace(/'/gi,"\"")).filter(isEnriched)
		} else {
			a["motifs"]=JSON.parse(row.motifs.replace(/'/gi,"\""))
		}
		a["TFs"]=JSON.parse(row.TFs.replace(/'/gi,"\""))
		}
                res.json(a);
		}
	});
})
var PosDb2 = new sqlite3.Database("data/mm10_one_tr_per_gene.motifs.sqlite3.db")
restapi.get('/mm10_cp_motifs', function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	PosDb2.get("SELECT * FROM tbl WHERE gene=?",req.query.gene,function(err,row){
		if(err) {
            		res.status(500);
			
		} else{
		var a={};
                if(row) {
		a["gene"]=row.gene
		if (req.query.enriched) {
			a["motifs"]=JSON.parse(row.motifs.replace(/'/gi,"\"")).filter(isEnriched)
		} else {
			a["motifs"]=JSON.parse(row.motifs.replace(/'/gi,"\""))
		}
                }
		res.json(a);
		}
	});
})

/** Section for homologene core promoter bl2seq result*/
var CP_bl2seq = new sqlite3.Database("data/CP.bl2seq.sqlite.db") 
restapi.get('/bl2seq_r',function(req,res) {
	res.setHeader("Access-Control-Allow-Origin", "*");
	var a=[];
	CP_bl2seq.each("SELECT * FROM bl2seq_r WHERE query_id=?",req.query.gene, function(err,row) {
		if(err) {
			res.status(500);
		} else {
			a.push(row)		
		}
	},function() {
	res.json(a)
	})
})
/** Section for Repeats **/

var hg19RepeatDb = new sqlite3.Database("data/hg19_corepromoter_repeats.db") 
restapi.get('/hg19_cp_repeats', function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	hg19RepeatDb.get("SELECT * FROM tbl WHERE gene=?",req.query.gene,function(err,row){
		if(err) {
            		res.status(500);
		} else {
		var a={};
                if(row) {
		a["gene"]=row.gene
		a["repeats"]=JSON.parse(row.repeats.replace(/'/gi,"\""))
		}
		res.json(a);
               
		}
	});
})

var mm10RepeatDb = new sqlite3.Database("data/mm10_corepromoter_repeats.db") 
restapi.get('/mm10_cp_repeats', function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	mm10RepeatDb.get("SELECT * FROM tbl WHERE gene=?",req.query.gene,function(err,row){
		if(err) {
            		res.status(500);
		} else {
		var a={};
                if(row){
		a["gene"]=row.gene
		a["repeats"]=JSON.parse(row.repeats.replace(/'/gi,"\""))
		}
		res.json(a);
		}
	});
})

restapi.get('/homolo_motifs',function(req,res) {
    	res.setHeader("Access-Control-Allow-Origin", "*");
	motifWeb.homoloMotifs(req.query.gene,function(d){
		res.json(d);
	})
})
restapi.listen(8081);