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|
//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2008 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#include <iostream>
#include <sstream>
#include "plink.h"
#include "helper.h"
#include "options.h"
#include "sockets.h"
using namespace std;
#define PORT_NUM 80
#define IP_ADDR "132.183.161.22"
void Plink::lookup()
{
#ifdef SKIP
printLOG("Web-lookup not implemented on this system...\n");
return;
#else
printLOG("PLINK-SNP (WGAS SNP annotation courtesy of Patrick Sullivan)\n");
vector<string> tokens;
vector< string > gene_list;
string GET_STRING;
if ( par::lookup_gene )
{
if ( par::lookup_multiple_genes )
{
string query = "";
int c = 0;
string window= int2str(par::lookup_snp_kb_window * 1000);
// Read list, append to query and send
checkFileExists(par::lookup_gene_name);
ifstream S(par::lookup_gene_name.c_str(),ios::in);
string cmd;
int x = 0;
GET_STRING = "GET /~purcell/cgi-bin/gene.pl?win=" + window;
while(!S.eof())
{
string gene;
S >> gene;
if (gene=="")
continue;
std::string s;
std::stringstream out;
out << x;
s = out.str();
cmd += "&gene" + s + "=" + gene;
x++;
c++;
gene_list.push_back(gene);
if ( c>100 )
error("Please do not send large batch queries to PLINK-SNP");
}
S.close();
GET_STRING += cmd + " HTTP/1.0 \n Content Length: 10000 \nHost: pngu.mgh.harvard.edu\nConnection: close\n\n";
tokens = socketConnection( this ,
IP_ADDR,
PORT_NUM,
GET_STRING );
}
else
{
string window = int2str( par::lookup_gene_kb_window * 1000 );
printLOG("Looking up gene information (and SNPs +/- "
+ int2str(par::lookup_gene_kb_window)+" kb)\n");
GET_STRING = "GET /~purcell/cgi-bin/gene.pl?win=" + window + "&gene=" + par::lookup_gene_name + " HTTP/1.0 \nHost: pngu.mgh.harvard.edu\nConnection: close\n\n";
tokens = socketConnection( this ,
IP_ADDR,
PORT_NUM,
GET_STRING );
}
}
else if ( par::lookup_single_snp )
{
string window= int2str(par::lookup_snp_kb_window * 1000);
printLOG("Looking up SNP information, listing genes within "
+ int2str(par::lookup_snp_kb_window)+" kb\n");
GET_STRING = "GET /~purcell/cgi-bin/snp.pl?win=" + window + "&snp=" + par::lookup_snp + " HTTP/1.0 \nHost: pngu.mgh.harvard.edu\nConnection: close\n\n";
tokens = socketConnection( this ,
IP_ADDR,
PORT_NUM,
GET_STRING );
}
else
{
string query = "";
int c = 0;
string window= int2str(par::lookup_snp_kb_window * 1000);
// Read list, append to query and send
checkFileExists(par::lookup_snp);
ifstream S(par::lookup_snp.c_str(),ios::in);
string cmd;
int x = 0;
GET_STRING = "GET /~purcell/cgi-bin/snp.pl?win=" + window;
while(!S.eof())
{
string snp;
S >> snp;
if (snp=="")
continue;
std::string s;
std::stringstream out;
out << x;
s = out.str();
cmd += "&snp" + s + "=" + snp;
x++;
c++;
if ( c>100 )
error("Please do not send large batch queries to PLINK-SNP");
}
S.close();
GET_STRING += cmd + " HTTP/1.0\nHost: pngu.mgh.harvard.edu\nConnection: close\n\n";
tokens = socketConnection( this ,
IP_ADDR,
PORT_NUM,
GET_STRING );
printLOG("Looking up SNP information, listing genes within "
+ int2str(par::lookup_snp_kb_window)+" kb)\n");
}
if ( tokens.size() < 25 ) {
cout << "\n\n";
if( par::lookup_single_snp )
cout << par::lookup_snp;
else
cout << par::lookup_gene_name;
cout << " not found\n";
cout << "-----------------------------\n";
return;
}
if ( par::lookup_to_file )
{
ofstream OUT;
string f = par::output_file_name;
// Need to handle both single and multiple instances
if ( par::lookup_gene )
{
f += ".snp.list";
if ( tokens[0] == "-1")
{
printLOG("\n\nCould not find gene "
+ par::lookup_gene_name
+ " in database\n");
return;
}
printLOG("Writing SNP details to [ " + f + " ]\n\n\n");
OUT.open( f.c_str(), ios::out );
bool geneInfo = true;
int totalSNPs = 0;
int gcount = 0;
for (int i=25; i<tokens.size()-1; i++)
{
if (tokens[i]=="__END")
{
// Skip following line return
if ( geneInfo )
{
// Move from gene information to SNPs
// if ( par::lookup_multiple_genes )
// OUT << tokens[i+1]; // "\n";
// OUT << gene_list[gcount++]; // << "\n";
geneInfo = false;
continue;
}
else
{
// Move from SNPs to gene information
// Skip count
++i;
geneInfo = true;
printLOG("----------------------------------------------------------\n");
printLOG("\n\n");
// if ( par::lookup_multiple_genes )
OUT << "END\n\n";
continue;
}
}
if ( geneInfo )
{
if (tokens[i]=="|n")
printLOG("\n");
else if ( tokens[i]=="|t")
printLOG("\t");
else
printLOG(tokens[i]+" ");
}
else
{
if (tokens[i]=="|n")
OUT << "\n";
else if ( tokens[i]=="|t")
OUT << "\t";
else
OUT << tokens[i] << " ";
}
}
OUT.close();
}
else // multiple SNP queries selected
{
f += ".snp.annot";
printLOG("\nWriting SNP details to [ " + f + " ]\n");
OUT.open( f.c_str(), ios::out );
for (int i=25; i<tokens.size()-1; i++)
{
if (tokens[i]=="|n")
OUT << "\n";
else if ( tokens[i]=="|t")
OUT << "\t";
else
OUT << tokens[i] << " ";
}
OUT.close();
}
}
else // Standard to LOG (single SNP query)
{
printLOG("\n\n");
for (int i=25; i<tokens.size()-1; i++)
{
if (tokens[i]=="|n")
printLOG("\n");
else if ( tokens[i]=="|t")
printLOG("\t");
else
printLOG(tokens[i]+" ");
}
}
return;
#endif
}
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