SNPResolver.sc: Retabbing document.

1 files changed, 190 insertions, 190 deletions

diff --git a/SNPResolver.sc b/SNPResolver.sc
index 777349c..9f368f0 100644
--- a/SNPResolver.sc
+++ b/SNPResolver.sc
@@ -1,196 +1,196 @@
 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);
-	}
+  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;
-	}
+  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;
-		}
-	}
+  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);	
-		});
-	}
+  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;
+  }
 
-	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]}
-				);
-			}
-		);
-	}
+  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]}
+        );
+      }
+    );
+  }
 }