{

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;

{

// 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