From 1bddd04f160644aca32fdb188752bdeaa99d4b8e Mon Sep 17 00:00:00 2001
From: David Runge <dave@sleepmap.de>
Date: Mon, 30 Mar 2015 02:31:58 +0200
Subject: SNPParser.sc: Retabbing document.

---
 SNPParser.sc | 200 +++++++++++++++++++++++++++++------------------------------
 1 file changed, 100 insertions(+), 100 deletions(-)

diff --git a/SNPParser.sc b/SNPParser.sc
index d3e89e9..6f33c63 100644
--- a/SNPParser.sc
+++ b/SNPParser.sc
@@ -1,107 +1,107 @@
 SNPParser{
-	var <placement;
-	var <comboDict;
-	var <file;
-	var <fileLength;
-	var <userID;
-	var <testSet;
+  var <placement;
+  var <comboDict;
+  var <file;
+  var <fileLength;
+  var <userID;
+  var <testSet;
 
-	*new{
-		arg aFile, aTestSet = inf;
-		^super.new.init(aFile, aTestSet);
-	}
+  *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;
-		});
-		userID.postln;
-	}
+  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;
+    });
+    userID.postln;
+  }
 
-	readFile{//parse the file this parser currently is setup with
-		var found = false, company = "";
-		"Guessing parser.".postln;
-		SNPInfo.sCompany.do({
-			arg cCompany, i;
-			if(file.contains(cCompany.asString),{
-				if(SNPInfo.workingSCompany.includes(i),{
-					("Attempting to parse a "++cCompany++" file now.").postln;
-					company = cCompany;
-					found = true;
-				},{
-					("Parsing files from "++cCompany++" is not supported (yet). Get me a coffee to make it work!").postln;
-				});
-			});
-		});
-		if(found.not,{
-			("This file might not be supported at all: "++file).postln;
-		},{
-			switch(company,
-				"23andme",{^this.parse23andme},
-				{"No no no no no!".postln}
-			);
-		});
-	}
+  readFile{//parse the file this parser currently is setup with
+    var found = false, company = "";
+    "Guessing parser.".postln;
+    SNPInfo.sCompany.do({
+      arg cCompany, i;
+      if(file.contains(cCompany.asString),{
+        if(SNPInfo.workingSCompany.includes(i),{
+          ("Attempting to parse a "++cCompany++" file now.").postln;
+          company = cCompany;
+          found = true;
+        },{
+          ("Parsing files from "++cCompany++" is not supported (yet). Get me a coffee to make it work!").postln;
+        });
+      });
+    });
+    if(found.not,{
+      ("This file might not be supported at all: "++file).postln;
+    },{
+      switch(company,
+        "23andme",{^this.parse23andme},
+        {"No no no no no!".postln}
+      );
+    });
+  }
 
-	parse23andme{//parsing a 23andme file: id, chromosome, position, base
-		var snpFile = File(file, "r"), line = "", counter = 0.0, tmp, snp, newSameCounter = 0.0;
-		fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
-		("File "++file++" is "++fileLength[0]++" lines long.").postln;
-		"Parsing might require some minutes! So kick back an get a coffee, while it lasts.".postln;
-		comboDict = SNPDict.new(fileLength[0], userID);
-		if(snpFile.isOpen,{
-			protect{
-				while{(line = snpFile.getLine).notNil}{//FIXME: Reinsert testset
-					if(line[0].asString!="#",{//skip commented lines
-						tmp = line.delimit({|ch| ch.isSpace});//delimit the line by space and/or tab
-						if(tmp[3].asString!="--" && (SNPInfo.isBasePair(tmp[3]) || SNPInfo.isBase(tmp[3]) && (SNPInfo.chromosomesLength[SNPInfo.convertChromosome(tmp[1])-1]>=tmp[2].asFloat)),{//skip empty SNPs and make sure it's either a single base or a base pair and ignore out-of-range SNPs (yes, science is unclear!)
-							if(SNPInfo.isBasePair(tmp[3]),{//if it's a base pair, set it up
-								snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], SNPInfo.createResolverForPair(tmp[3]));
-							},{
-								if(SNPInfo.isBase(tmp[3]), {//if it's a single base, set it up
-									snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], \none);
-								});
-							});
-							newSameCounter = newSameCounter + comboDict.storeSNP(snp, SNPInfo.calcPosition(snp.chromosome, snp.position));
-							switch(newSameCounter,
-								1.0,{"Storing SNPs now: \n==========".postln;},
-								100000.0,{"=".post;},
-								200000.0,{"=".post;},
-								300000.0,{"=".post;},
-								400000.0,{"=".post;},
-								500000.0,{"=".post;},
-								600000.0,{"=".post;},
-								700000.0,{"=".post;},
-								800000.0,{"=".post;},
-								900000.0,{"=".post;},
-							);
-						});
-					});
-				counter = counter + 1;
-				};
-			}{
-				snpFile.close;
-			};
-		},{
-			("Couldn't open file for reading: "++file).warn;
-		});
-		"=".postln;
-		"Sorting lookup tables. This will also take some time!".postln;
-		comboDict.orderLookup(2);
-		"Done sorting lookup tables.".postln;
-		^comboDict;
-	}
+  parse23andme{//parsing a 23andme file: id, chromosome, position, base
+    var snpFile = File(file, "r"), line = "", counter = 0.0, tmp, snp, newSameCounter = 0.0;
+    fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
+    ("File "++file++" is "++fileLength[0]++" lines long.").postln;
+    "Parsing might require some minutes! So kick back an get a coffee, while it lasts.".postln;
+    comboDict = SNPDict.new(fileLength[0], userID);
+    if(snpFile.isOpen,{
+      protect{
+        while{(line = snpFile.getLine).notNil}{//FIXME: Reinsert testset
+          if(line[0].asString!="#",{//skip commented lines
+            tmp = line.delimit({|ch| ch.isSpace});//delimit the line by space and/or tab
+            if(tmp[3].asString!="--" && (SNPInfo.isBasePair(tmp[3]) || SNPInfo.isBase(tmp[3]) && (SNPInfo.chromosomesLength[SNPInfo.convertChromosome(tmp[1])-1]>=tmp[2].asFloat)),{//skip empty SNPs and make sure it's either a single base or a base pair and ignore out-of-range SNPs (yes, science is unclear!)
+              if(SNPInfo.isBasePair(tmp[3]),{//if it's a base pair, set it up
+                snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], SNPInfo.createResolverForPair(tmp[3]));
+              },{
+                if(SNPInfo.isBase(tmp[3]), {//if it's a single base, set it up
+                  snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], \none);
+                });
+              });
+              newSameCounter = newSameCounter + comboDict.storeSNP(snp, SNPInfo.calcPosition(snp.chromosome, snp.position));
+              switch(newSameCounter,
+                1.0,{"Storing SNPs now: \n==========".postln;},
+                100000.0,{"=".post;},
+                200000.0,{"=".post;},
+                300000.0,{"=".post;},
+                400000.0,{"=".post;},
+                500000.0,{"=".post;},
+                600000.0,{"=".post;},
+                700000.0,{"=".post;},
+                800000.0,{"=".post;},
+                900000.0,{"=".post;},
+              );
+            });
+          });
+        counter = counter + 1;
+        };
+      }{
+        snpFile.close;
+      };
+    },{
+      ("Couldn't open file for reading: "++file).warn;
+    });
+    "=".postln;
+    "Sorting lookup tables. This will also take some time!".postln;
+    comboDict.orderLookup(2);
+    "Done sorting lookup tables.".postln;
+    ^comboDict;
+  }
 }
-- 
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