Classes and howto

1 files changed, 196 insertions, 0 deletions

diff --git a/SNPResolver.sc b/SNPResolver.sc
new file mode 100644
index 0000000..777349c
--- /dev/null
+++ b/SNPResolver.sc
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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]}
+				);
+			}
+		);
+	}
+}