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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2009 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"
#include "nlist.h"
using namespace std;
#define PORT_NUM 80
#define IP_ADDR "152.19.78.148"
void convertPosition(string pquery, int & chr, int & bp1, int & bp2, bool useKb, bool useMb)
{
size_t p1 = pquery.find(":");
size_t p2 = pquery.find("-");
if ( p1 == string::npos || p2 == string::npos || p1 >= p2 )
error("Badly formed positional query: " + pquery );
string ccode = pquery.substr(0,p1);
if ( ccode.size() < 4 )
error("Badly formed positional query: " + pquery );
if ( ccode.substr(0,3) != "chr" )
error("Badly formed positional query: " + pquery );
if ( ! from_string<int>( chr , ccode.substr(3) , std::dec ) )
error("Badly formed positional query: " + pquery );
string p1code = pquery.substr(p1+1,p2-p1-1);
double pp1;
if ( ! from_string<double>( pp1 , p1code , std::dec ) )
error("Badly formed positional query: " + pquery );
string p2code = pquery.substr(p2+1);
double pp2;
if ( ! from_string<double>( pp2 , p2code , std::dec ) )
error("Badly formed positional query: " + pquery );
if ( useKb )
{
bp1 = int(pp1 * 1000);
bp2 = int(pp2 * 1000);
}
else if ( useMb )
{
bp1 = int(pp1 * 1000000);
bp2 = int(pp2 * 1000000);
}
else
{
bp1 = int(pp1);
bp2 = int(pp2);
}
// Possible overflow
if ( bp1 < 0 ) bp1 = 0;
if ( bp2 < 0 ) bp2 = 0;
}
void Plink::lookup2()
{
// In general, for these lookups, we do not want to treat the
// minus/hyphen character as a range delimiter in the normal
// sense. It will be specially handled for chr1:1-100 values; also,
// it might appear in gene names, e.g. HLA-A. By setting the range
// character to a space, we essentially ensure that we will never
// encounter it. Because we shutdown() after performing this
// analysis, we do not need to worry about other operations getting
// messed up.
par::range_delimiter = " ";
#ifdef SKIP
printLOG("Web-lookup not implemented on this system...\n");
return;
#else
// printLOG("PLINK-SNP (WGAS SNP annotation courtesy of Patrick Sullivan)\n");
// http://sullivanlab.unc.edu/plink/snp.php?rsid=rs12345,rs67890&gene=DISC1,CACNA1C&exon=1&cnv=0
// http://sullivanlab.unc.edu/plink/genelist.php?&searchtype=gn&gene=COMT,GTF2H2,FURBERG,AMY1,AMY2B
// http://sullivanlab.unc.edu/plink/genelist.php?searchtype=gp&chr=6&start=30000000&end=30500000
// { rsid = rs12345 OR rsid = rs67890 }
// AND { exon = true }
// AND { cnv = false }
// AND { gene = DISC1 OR gene = CACNA1C }
string GET_STRING;
string command;
// Lookup genes
// # 'pos' key -- default is BP
// --lookup-gene [pos,mb] chr18:30.2-30.2
// --lookup-gene [pos,kb] chr18:30200-302809
// --lookup-gene [pos] chr18:30200000-30280900
// # list
// --lookup-gene [file] mygenes.lst
// --lookup-gene [list] mygenes.lst
// # name
// --lookup-gene CACNA1C
// --lookup-gene [name] CACNA1C
// # query
// --lookup-gene [query] gset=GO_363526,pos=chr6:30200000-30280900,list=mygenes.lst,gene=CACNA1C
// --lookup-gene [pos] chr18:
// Agreed keywords
OptionSet * lookup2_opt = par::opt.getOptions("LOOKUP");
bool useMb = lookup2_opt->isSet("mb")
|| lookup2_opt->isSet("Mb")
|| lookup2_opt->isSet("MB");
bool useKb = lookup2_opt->isSet("kb")
|| lookup2_opt->isSet("Kb")
|| lookup2_opt->isSet("KB");
if ( useMb && useKb )
error("Cannot specify both Mb and Kb positional queries");
// A query
if ( lookup2_opt->isSet("query") )
{
NList nl(0);
NList tlist(0);
vector<string> ids = tlist.deparseStringList( par::lookup2_cmd );
for (int i = 0 ; i < ids.size(); i++)
{
string pquery = ids[i];
// Expect format : X=Y
size_t p1 = pquery.find("=");
string key,val;
if (p1==string::npos)
{
key = pquery;
val = "=1";
}
else
{
key = pquery.substr(0,p1+1);
val = pquery.substr(p1+1);
if ( key=="pos=" )
{
int chr, bp1, bp2;
convertPosition(val,chr,bp1,bp2,useKb,useMb);
val = int2str(chr) + "," + int2str( (int)bp1 ) + "," + int2str( (int)bp2 );
}
}
if ( i == 0 )
command += key + val;
else
command += "&"+ key + val;
}
}
else if ( lookup2_opt->isSet("pos"))
{
// Positional query
// Assume a comma delimited list in format:
// chr2:737-3993
NList nl(0);
NList tlist(0);
vector<string> ids = tlist.deparseStringList( par::lookup2_cmd );
for (int i = 0 ; i < ids.size(); i++)
{
// Always requires format X:Y-Z
// X should start "chrXX"
// Y should be a number
// Z should also be a number
string pquery = ids[i];
int chr, bp1, bp2;
convertPosition(pquery,chr,bp1,bp2,useKb,useMb);
pquery = "pos=" + int2str(chr) + "," + int2str( (int)bp1 ) + "," + int2str( (int)bp2 );
if ( i == 0 )
command += pquery;
else
command += "&"+pquery;
}
}
else if ( lookup2_opt->isSet("list") || lookup2_opt->isSet("file") )
{
checkFileExists(par::lookup2_cmd );
ifstream IN1( par::lookup2_cmd.c_str() , ios::in );
command = par::lookup_gene ? "gene=" : "rsid=";
bool doneFirst = false;
while ( ! IN1.eof() )
{
string name;
IN1 >> name;
if ( name == "" )
continue;
if ( ! doneFirst )
{
command += name;
doneFirst = true;
}
else
command += "," + name;
}
IN1.close();
}
else if ( lookup2_opt->isSet("qfile") || lookup2_opt->isSet("qlist") )
{
checkFileExists(par::lookup2_cmd);
ifstream IN1( par::lookup2_cmd.c_str() , ios::in );
bool doneFirst = false;
while ( ! IN1.eof() )
{
vector<string> tok = tokenizeLine(IN1);
if ( tok.size() == 0 )
continue;
if ( tok.size() != 2 )
error("Problem with query file: not 2 columns");
string key = tok[0];
string val = tok[1];
if ( ! doneFirst )
{
command += key + "=" + val;
doneFirst = true;
}
else
command += "&" + key + "=" + val;
}
IN1.close();
}
else // assume simple gene-name query
{
command = par::lookup_gene ? "gene=" : "rsid=";
NList nl(0);
NList tlist(0);
vector<string> ids = tlist.deparseStringList( par::lookup2_cmd );
for (int i = 0 ; i < ids.size(); i++)
{
if ( ids[i].find("=") != string::npos )
error("Badly formed gene name, with equals sign '=' in it -- did you mean to add [query]?");
if ( i == 0 )
command += ids[i];
else
command += ","+ids[i];
}
}
if ( par::lookup_gene )
GET_STRING = "GET /plink/genelist.php?";
else
GET_STRING = "GET /plink/snplist.php?";
GET_STRING += command;
// GET_STRING += "searchtype=gp&chr=6&start=30000000&end=30500000";
cout << "Proposed command = \n";
cout << GET_STRING << "\n";
GET_STRING += "\nHTTP/1.0\nContent Length: 10000\nHost: 152.19.78.148\nConnection: close\n\n";
cout << "GET_STRING:\n\n" << GET_STRING << "\n";
////////////////////////////////////////////////
// Make database call
vector<string> tokens = socketConnection( this ,
IP_ADDR,
PORT_NUM,
GET_STRING );
////////////////////////////////////////////////
// Relay output
cout << "Output = \n";
for (int t = 0 ; t < tokens.size() ; t++)
{
cout << "token[" << t << "] = [ " << tokens[t] << "]\n";
}
cout << "\n";
cout << "-------------------------------\n";
#endif
}
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