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SNPResolver{
var <fileEnd = ".json";
var <idList = "";
var <userID;
var <thisUser;
var <users;
var <usersWithGenotypes = 0;
var <file;
var <path;
var <>resolver;
//initialize with a path to write json files to (/tmp for example), with a minimum free disk space of ~17-25GB!
*new{
arg aPath = "/tmp/theSoundOfPeople/", aID = 1;
^super.new.init(aPath, aID);
}
init{
arg aPath, aID;
path = aPath;
userID = aID.asInt;
if(File.exists(path++userID++"/").not, {
protect{
File.mkdir(path++userID++"/");
}{
("Oh noes. The directory '"++this.path++"' could not be created. Check if all parent dirs are there and you have write permission!").warn;
};
});
// this.downloadUserList;
}
downloadUserList{//download a new users.json and parse it for users with genotypes
var usersFinished = Condition.new(false);
var phenoFinished = Condition.new(false);
fork{
("Downloading user list to: "++path++userID.asString++"/"++"users"++fileEnd).postln;
("curl -s -o "++path++userID.asString++"/"++"users"++fileEnd++" http://opensnp.org/users"++fileEnd).unixCmd({
arg res,pid;
if(res.asInt!=0,{
"Server down. Try again later!".postln
},{//if the download finished, resume with parsing
usersFinished.unhang;
});
}, false);//save to file with user id as parentdir
usersFinished.hang;
"Extracting users with genotypes...".postln;
users = (path++userID.asString++"/"++"users"++fileEnd).asString.parseYAMLFile;
users.do({//retrieve the user IDs of users that uploaded genotypes
arg item, i;
if(users[i].at("genotypes")[0].notNil,{
if(users[i].at("id").asInt!=userID, {//exclude the user we're currently working on
idList = idList ++ users[i].at("id").asString++",";
usersWithGenotypes = usersWithGenotypes + 1;
});
});
});
idList.removeAt(idList.size-1);//remove the last ","
"Done".postln;
("Downloading user phenotype information to: "++path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd).postln;
("curl -s -o "++path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd++" http://opensnp.org/phenotypes/json/"++userID.asString++fileEnd.asString).unixCmd({
arg res,pid;
if(res.asInt!=0,{
"Server down. Try again later!".postln
},{//if the download finished, resume with parsing
phenoFinished.unhang;
});
}, false);//save to file with user id as parentdir
phenoFinished.hang;
thisUser = (path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd).asString.parseYAMLFile;
("Finished downloading phenotypes of "++thisUser.at("user").at("name").asString++".").postln;
}
}
downloadResolver{//get a resolver for an ID (of a base pair at a certain position) from opensnp.org
arg id;
var state = false; //, downloadFinished = Condition.new(false);
if(File.exists(path++userID.asString++"/"++id.asString++fileEnd).not,{
("Downloading JSON file for "++id).postln;
("curl -s -o "++path++userID.asString++"/"++id.asString++fileEnd++" http://opensnp.org/snps/"++id.asString++fileEnd).unixCmd({
arg res,pid;
if(res.asInt!=0,{
"Failed! Retry later.".postln;
},{
"Success!".postln;
});
},false);//save to file with user id as parent directory
state = true;
},{
state = true;
});
^state;
}
retrieveResolver{//parse a downloaded JSON file and retrieve a resolver for a given base (pair) with an ID. Returns resolver base or \none
arg snp, id;
var baseCase = 0;
if(File.exists(path++userID.asString++"/"++id.asString++fileEnd),{//if the json file exists, parse it and return the resolver (if found)
var matchHunt = 0, huntOver = false, jsonReturn, resolver, jsonFile;
jsonFile = (path++userID.asString++"/"++id.asString++fileEnd);
try{
jsonReturn = jsonFile.parseYAMLFile;//parse the JSON file
while({ matchHunt < size(jsonReturn) && huntOver.not },{//iterate the parsed JSON for a combo match
if(jsonReturn[matchHunt].includesKey("error").not,{//if error, skip this one
if(size(jsonReturn[matchHunt].at("user").at("genotypes"))!=0,{//if there is no data, skip this one
if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != "--",{//if it's invalid (too), skip this one
if(SNPInfo.isBase(snp),{//check if single base or base pair
baseCase = 1;
});
switch(baseCase,
0,{//base pair lookup
if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != snp.asString && SNPInfo.isBasePair(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype")),{//check if it's member of base pair and not the same base pair
("SUCCESS: Different base found for "++id.asString++" in ("++(matchHunt+1).asString++"/"++jsonReturn.size.asString++")!").post;
(snp.asString++" -> "++jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString).postln;
resolver = this.calcResolverPair(snp, jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asSymbol);
huntOver = true;
});
},
1,{//single base lookup
if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != snp.asString && SNPInfo.isBase(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype")),{//check if it's member of base pair and not the same base pair
("SUCCESS: Different base found for "++id.asString++" in ("++(matchHunt+1).asString++"/"++jsonReturn.size.asString++")!").post;
(snp.asString++" -> "++jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString).postln;
resolver = [jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asSymbol];
huntOver = true;
});
}
);
});
});
});
matchHunt = matchHunt + 1;
});
jsonReturn = nil;
if(resolver.isNil,{//if no resolver was found return none
switch(baseCase,
0,{^SNPInfo.emptyBasePair},
1,{^SNPInfo.emptyBase}
);
},{
^resolver;
});
}{
("FAILED: Parsing not possible, file corrupt: "++id.asString++fileEnd).postln;
("Skipping for now and removing.").postln;
File.delete(path++userID.asString++"/"++id.asString++fileEnd);
}
},{//file is not there yet, download it? something like that...
("FAILED: Resolver file for "++id.asString++" not available yet. Download it.").postln;
// this.downloadResolver(id);
});
}
calcResolverPair{//calculate upper/lower ends of resolver pairs
arg base, resolver;
switch(base,
\AA,{
switch(resolver,
\AC,{^[resolver,\CC]},
\CC,{^[\AC,resolver]},
\AG,{^[resolver,\GG]},
\GG,{^[\AG,resolver]},
\AT,{^[resolver,\TT]},
\TT,{^[\AT,resolver]}
);
},
\CC,{
switch(resolver,
\AA,{^[resolver,\AC]},
\AC,{^[\AA,resolver]},
\CG,{^[resolver,\GG]},
\GG,{^[\CG,resolver]},
\CT,{^[resolver,\TT]},
\TT,{^[\CT,resolver]}
);
},
\GG,{
switch(resolver,
\AA,{^[resolver,\AG]},
\AG,{^[\AA,resolver]},
\CG,{^[\CC,resolver]},
\CC,{^[resolver,\CG]},
\GT,{^[resolver,\TT]},
\TT,{^[\GT,resolver]}
);
},
\TT,{
switch(resolver,
\AA,{^[resolver,\AT]},
\AT,{^[\AA,resolver]},
\CT,{^[\CC,resolver]},
\CC,{^[resolver,\CT]},
\GT,{^[\GG,resolver]},
\GG,{^[resolver,\GT]}
);
}
);
}
}
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