From c7b922ec7a9aab0599a9abe6d36c8168dde7a884 Mon Sep 17 00:00:00 2001
From: David Runge <dave@sleepmap.de>
Date: Mon, 30 Mar 2015 02:31:25 +0200
Subject: SNPFile.sc: Retabbing document.

---
 SNPFile.sc | 317 ++++++++++++++++++++++++++++++-------------------------------
 1 file changed, 158 insertions(+), 159 deletions(-)

diff --git a/SNPFile.sc b/SNPFile.sc
index a811d6f..22505b0 100644
--- a/SNPFile.sc
+++ b/SNPFile.sc
@@ -1,167 +1,166 @@
 SNPFile{
-	var <snpDict;
-	var <file;
-	var <fileLength;
-	var <userID;
-	var <testSet = inf;
-	*new{
-		arg aFile, aTestSet = inf;
-		^super.new.init(aFile, aTestSet);
-	}
+  var <snpDict;
+  var <file;
+  var <fileLength;
+  var <userID;
+  var <testSet = inf;
+  *new{
+    arg aFile, aTestSet = inf;
+    ^super.new.init(aFile, aTestSet);
+  }
 
-	init{
-		arg aFile, aTestSet;
-		this.setFileAndUser(aFile);
-		testSet = aTestSet;
-	}
+  init{
+    arg aFile, aTestSet;
+    this.setFileAndUser(aFile);
+    testSet = aTestSet;
+  }
 
-	
-	setFileAndUser{//set the file (again) to be parsed
-		arg aFile;
-		var allSlash, allDot;
-		file = aFile;
-		allSlash = file.findAll("/");
-		allDot = file.findAll(".");
-		if(allSlash.notNil,{//if there is no slash in the filename
-			userID = file[allSlash[allSlash.size-1]+1..allDot[allDot.size-2]-1].asInt;
-		},{
-			userID = file[0..allDot[allDot.size-2]-1].asInt;
-		});
-	}
+  setFileAndUser{//set the file (again) to be parsed
+    arg aFile;
+    var allSlash, allDot;
+    file = aFile;
+    allSlash = file.findAll("/");
+    allDot = file.findAll(".");
+    if(allSlash.notNil,{//if there is no slash in the filename
+      userID = file[allSlash[allSlash.size-1]+1..allDot[allDot.size-2]-1].asInt;
+    },{
+      userID = file[0..allDot[allDot.size-2]-1].asInt;
+    });
+  }
 
-	readFile{//read a SNPDict from file
-		var snpFile = File(file, "r"), line = "", counter = 0, procCounter = Array.new(9), tmp, key, sizeOf, snp, res, keyCount = 0.0, unknown, unknownCount = 0.0;
-		fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
-		9.do({|item,i| procCounter.add(round((fileLength[0].asFloat/100)*(i+1)*10, 1).asInt)});//calculating procentuals for a simple progression output
-		("Now reading: "++file++" ("++fileLength[0]++" lines).").postln;
-		("==========").postln;
-		if(snpFile.isOpen,{
-			protect{
-				while{(line = snpFile.getLine).notNil }{
-					switch(line[0].asString, 
-						"*",{//info line
-							sizeOf = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
-							snpDict = SNPDict.new(sizeOf[1].asFloat, sizeOf[3].asInt);//init new SNPDict
-							snpDict.initLookupFromFile(sizeOf[1].asFloat, sizeOf[2].asFloat);
-						},
-						";",{//key line
-							key = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
-							snpDict.addPositionLookupFromFile(keyCount, key[1].asFloat);//store to lookup table!
-							keyCount = keyCount + 1.0;
-						},
-						"+",{//SNP line
-							tmp = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
-							if(tmp[6].isNil,{
-								res = [tmp[5].asSymbol];
-							},{
-								res = [tmp[5].asSymbol, tmp[6].asSymbol];
-							});
-							snp = SNP.new(tmp[1], tmp[2], tmp[3], tmp[4], res);
-							snpDict.storeSNP(snp, key[1]);
-						},
-						"|",{//unknown line
-							unknown = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
-							snpDict.addUnknownLookupFromFile(unknownCount, unknown[1].asFloat);
-							unknownCount = unknownCount + 1.0;
-						}
-					);
-					counter = counter + 1;
-					switch(counter,
-						procCounter[0],{"=".post;},
-						procCounter[1],{"=".post;},
-						procCounter[2],{"=".post;},
-						procCounter[3],{"=".post;},
-						procCounter[4],{"=".post;},
-						procCounter[5],{"=".post;},
-						procCounter[6],{"=".post;},
-						procCounter[7],{"=".post;},
-						procCounter[8],{"=".post;}
-					);
-				};
-			"=".postln;
-			"Done reading file to RAM.".postln;
-			}{
-				snpFile.close;
-			};
-		},{
-			("Couldn't open file for reading: "++file).warn;
-		});
-		^snpDict;
-	}
+  readFile{//read a SNPDict from file
+    var snpFile = File(file, "r"), line = "", counter = 0, procCounter = Array.new(9), tmp, key, sizeOf, snp, res, keyCount = 0.0, unknown, unknownCount = 0.0;
+    fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
+    9.do({|item,i| procCounter.add(round((fileLength[0].asFloat/100)*(i+1)*10, 1).asInt)});//calculating procentuals for a simple progression output
+    ("Now reading: "++file++" ("++fileLength[0]++" lines).").postln;
+    ("==========").postln;
+    if(snpFile.isOpen,{
+      protect{
+        while{(line = snpFile.getLine).notNil }{
+          switch(line[0].asString, 
+            "*",{//info line
+              sizeOf = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
+              snpDict = SNPDict.new(sizeOf[1].asFloat, sizeOf[3].asInt);//init new SNPDict
+              snpDict.initLookupFromFile(sizeOf[1].asFloat, sizeOf[2].asFloat);
+            },
+            ";",{//key line
+              key = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
+              snpDict.addPositionLookupFromFile(keyCount, key[1].asFloat);//store to lookup table!
+              keyCount = keyCount + 1.0;
+            },
+            "+",{//SNP line
+              tmp = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
+              if(tmp[6].isNil,{
+                res = [tmp[5].asSymbol];
+              },{
+                res = [tmp[5].asSymbol, tmp[6].asSymbol];
+              });
+              snp = SNP.new(tmp[1], tmp[2], tmp[3], tmp[4], res);
+              snpDict.storeSNP(snp, key[1]);
+            },
+            "|",{//unknown line
+              unknown = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
+              snpDict.addUnknownLookupFromFile(unknownCount, unknown[1].asFloat);
+              unknownCount = unknownCount + 1.0;
+            }
+          );
+          counter = counter + 1;
+          switch(counter,
+            procCounter[0],{"=".post;},
+            procCounter[1],{"=".post;},
+            procCounter[2],{"=".post;},
+            procCounter[3],{"=".post;},
+            procCounter[4],{"=".post;},
+            procCounter[5],{"=".post;},
+            procCounter[6],{"=".post;},
+            procCounter[7],{"=".post;},
+            procCounter[8],{"=".post;}
+          );
+        };
+      "=".postln;
+      "Done reading file to RAM.".postln;
+      }{
+        snpFile.close;
+      };
+    },{
+      ("Couldn't open file for reading: "++file).warn;
+    });
+    ^snpDict;
+  }
 
-	writeFile{//write a SNPDict to file
-		arg snpDict;
-		var snpFile = File(file, "w"), line = "", counter = 0, tmp, snp, newSameCounter = 0;
-		("Attempting to write SNPDict to file: "++file).postln;
-		if(snpFile.isOpen, {
-			protect{
-				snpFile.write("*\t"++snpDict.snpArr.size.asString++"\t"++snpDict.unknownArr.size.asString++"\t"++snpDict.userID++"\n");//write length of snpArr and unknownArr
-				snpDict.snpArr.do({
-					arg item;
-					snpFile.write(";\t"++item.asString++"\n");
-					snpDict.snpAtPosition(item).do({//write all SNPs
-						arg snp;
-						var res;
-						if(snp.resolver.size==2,{
-							res = (snp.resolver[0]++"\t"++snp.resolver[1]).asString;
-						},{
-							res = snp.resolver[0].asString;
-						});
-						snpFile.write("+\t"++snp.chromosome.asString++"\t"++snp.position.asString++"\t"++snp.id.asString++"\t"++snp.base.asString++"\t"++res++"\n");//write SNP to file 
-					});
-				});
-				snpDict.unknownArr.do({//write all unknown positions
-					arg item;
-					snpFile.write("|\t"++item.asString++"\n");
-				});
-			}{
-				snpFile.close;
-				("Done writing to file.").postln;
-				^true;
-			};
-		},{
-			("Couldn't open file for writing: "++file).postln;
-			^false;
-		});
-	}
+  writeFile{//write a SNPDict to file
+    arg snpDict;
+    var snpFile = File(file, "w"), line = "", counter = 0, tmp, snp, newSameCounter = 0;
+    ("Attempting to write SNPDict to file: "++file).postln;
+    if(snpFile.isOpen, {
+      protect{
+        snpFile.write("*\t"++snpDict.snpArr.size.asString++"\t"++snpDict.unknownArr.size.asString++"\t"++snpDict.userID++"\n");//write length of snpArr and unknownArr
+        snpDict.snpArr.do({
+          arg item;
+          snpFile.write(";\t"++item.asString++"\n");
+          snpDict.snpAtPosition(item).do({//write all SNPs
+            arg snp;
+            var res;
+            if(snp.resolver.size==2,{
+              res = (snp.resolver[0]++"\t"++snp.resolver[1]).asString;
+            },{
+              res = snp.resolver[0].asString;
+            });
+            snpFile.write("+\t"++snp.chromosome.asString++"\t"++snp.position.asString++"\t"++snp.id.asString++"\t"++snp.base.asString++"\t"++res++"\n");//write SNP to file 
+          });
+        });
+        snpDict.unknownArr.do({//write all unknown positions
+          arg item;
+          snpFile.write("|\t"++item.asString++"\n");
+        });
+      }{
+        snpFile.close;
+        ("Done writing to file.").postln;
+        ^true;
+      };
+    },{
+      ("Couldn't open file for writing: "++file).postln;
+      ^false;
+    });
+  }
 
-	writeUnknownIDToFile{//write the rsids of all unknown SNPs to file
-		arg snpDict;
-		var snpFile = File("/media/Data/tmp/1/1.unknown.snp", "w");
-		("Attempting to write unknowns to file: "++file).postln;
-		if(snpFile.isOpen, {
-			protect{
-				snpDict.unknownArr.do({
-					arg item,i;
-					snpDict.noneResolverAtPosition(item).do({
-						arg snp,i;
-						snpFile.write(snp.id++"\n");
-					});
-				});
-			}
-		},{
-			("Couldn't open file for writing: "++file).postln;
-			^false;
-		});
-	}
+  writeUnknownIDToFile{//write the rsids of all unknown SNPs to file
+    arg snpDict;
+    var snpFile = File("/media/Data/tmp/1/1.unknown.snp", "w");
+    ("Attempting to write unknowns to file: "++file).postln;
+    if(snpFile.isOpen, {
+      protect{
+        snpDict.unknownArr.do({
+          arg item,i;
+          snpDict.noneResolverAtPosition(item).do({
+            arg snp,i;
+            snpFile.write(snp.id++"\n");
+          });
+        });
+      }
+    },{
+      ("Couldn't open file for writing: "++file).postln;
+      ^false;
+    });
+  }
 
-	readUnknownIDFromFile{
-		arg unknowns;
-		var snpFile = File(unknowns, "r"), fileLength, line ="", outArr, counter = 0;
-		fileLength = (("wc -l "++unknowns.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
-		fileLength.postln;
-		outArr = Array.new(fileLength[0].asInt);
-		if(snpFile.isOpen, {
-			protect{
-				while{(line = snpFile.getLine).notNil }{
-					outArr.add(line.asSymbol);
-					counter = counter + 1;
-				}
-			}
-			^outArr;
-		},{
-			("Couldn't open file for writing: "++file).postln;
-			^false;
-		});
-	}
+  readUnknownIDFromFile{
+    arg unknowns;
+    var snpFile = File(unknowns, "r"), fileLength, line ="", outArr, counter = 0;
+    fileLength = (("wc -l "++unknowns.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
+    fileLength.postln;
+    outArr = Array.new(fileLength[0].asInt);
+    if(snpFile.isOpen, {
+      protect{
+        while{(line = snpFile.getLine).notNil }{
+          outArr.add(line.asSymbol);
+          counter = counter + 1;
+        }
+      }
+      ^outArr;
+    },{
+      ("Couldn't open file for writing: "++file).postln;
+      ^false;
+    });
+  }
 }
-- 
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