Parsing a genomic position with javacc
Parsing a genomic position (chrom:start-end) is an easy task but I've always been too lazy to create a library for this. Today I wrote a Java-CC-based parser for analyzing the various syntaxes of a genomic position. Here is the grammar I used:
COMMA: ","
LETTER: (["a"-"z"]|["A"-"Z"]|"_") ;
DIGIT: ["0"-"9"];
INT:<DIGIT> ( (<DIGIT>|<COMMA>)* <DIGIT>)? ;
BP: "b" ("p")? ;
KB: ("k") ("B")? ;
MB: ("m") ("B")? ;
GB: ("g") ("B")? ;
IDENTIFIER: <LETTER> (<DIGIT>|<LETTER>)* ;
COLON: ":" ;
DASH: "-" ;
PLUS: "+" ;
DELIM: ("|"|";") ;
java.util.List<Segment> many(): segment() ((<DELIM>)? segment() )* )? <EOF>);
Segment one(): segment() <EOF>;
Segment segment(): chromName() <COLON> position() (<DASH> position()| <PLUS> position())? );
BigInteger position():integer() (factor())?;
BigInteger factor(): ( <BP> | <KB>| <MB> | <GB> );
BigInteger integer():<INT> ;
String chromName():( integer() | identifier());
String identifier(): <IDENTIFIER> ;
LETTER: (["a"-"z"]|["A"-"Z"]|"_") ;
DIGIT: ["0"-"9"];
INT:<DIGIT> ( (<DIGIT>|<COMMA>)* <DIGIT>)? ;
BP: "b" ("p")? ;
KB: ("k") ("B")? ;
MB: ("m") ("B")? ;
GB: ("g") ("B")? ;
IDENTIFIER: <LETTER> (<DIGIT>|<LETTER>)* ;
COLON: ":" ;
DASH: "-" ;
PLUS: "+" ;
DELIM: ("|"|";") ;
java.util.List<Segment> many(): segment() ((<DELIM>)? segment() )* )? <EOF>);
Segment one(): segment() <EOF>;
Segment segment(): chromName() <COLON> position() (<DASH> position()| <PLUS> position())? );
BigInteger position():integer() (factor())?;
BigInteger factor(): ( <BP> | <KB>| <MB> | <GB> );
BigInteger integer():<INT> ;
String chromName():( integer() | identifier());
String identifier(): <IDENTIFIER> ;
Source code
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| options { | |
| static=false; | |
| DEBUG_PARSER=false; | |
| IGNORE_CASE=true; | |
| } | |
| PARSER_BEGIN(SegmentParser) | |
| /** | |
| * Author: | |
| * Pierre Lindenbaum PhD | |
| * WWW | |
| * http://plindenbaum.blogspot.com | |
| * Motivation | |
| * parsing a genomic fragment (chr:start-end) | |
| * Compilation | |
| * javacc SegmentParser.jj | |
| * javac -Xlint:unchecked SegmentParser.java | |
| * echo " chrM:1-100,000"| java SegmentParser | |
| */ | |
| import java.math.BigInteger; | |
| class Segment | |
| { | |
| String chrom; | |
| int start; | |
| int end; | |
| public Segment(String chrom,int start,int end) | |
| { | |
| this.chrom=chrom; | |
| this.start=start; | |
| this.end=end; | |
| } | |
| public String toString() | |
| { | |
| return chrom+":"+start+"-"+end; | |
| } | |
| } | |
| public class SegmentParser | |
| { | |
| private static final BigInteger TWO=new BigInteger("2"); | |
| private static final BigInteger INT_MAX=new BigInteger(String.valueOf(Integer.MAX_VALUE)); | |
| public static Segment parseOne(String s) | |
| { | |
| try | |
| { | |
| SegmentParser parser = new SegmentParser(new java.io.StringReader(s)); | |
| return parser.one(); | |
| } | |
| catch(ParseException err) | |
| { | |
| throw new IllegalArgumentException(err); | |
| } | |
| } | |
| public static java.util.List<Segment> parseMany(String s) | |
| { | |
| try | |
| { | |
| SegmentParser parser = new SegmentParser(new java.io.StringReader(s)); | |
| return parser.many(); | |
| } | |
| catch(ParseException err) | |
| { | |
| throw new IllegalArgumentException(err); | |
| } | |
| } | |
| public static void main(String args[]) | |
| { | |
| try | |
| { | |
| SegmentParser parser = new SegmentParser(System.in); | |
| System.out.println(parser.one()); | |
| } | |
| catch(Throwable err) | |
| { | |
| err.printStackTrace(); | |
| } | |
| } | |
| } | |
| PARSER_END(SegmentParser) | |
| SKIP:{ | |
| " "|"\n" | |
| } | |
| TOKEN: | |
| { | |
| <#COMMA: ","> | |
| | <#LETTER:(["a"-"z"]|["A"-"Z"]|"_")> | |
| | <#DIGIT:["0"-"9"]> | |
| | <INT:<DIGIT> ( (<DIGIT>|<COMMA>)* <DIGIT>)? > | |
| | <BP: "b" ("p")?> | |
| | <KB: ("k") ("B")?> | |
| | <MB: ("m") ("B")?> | |
| | <GB: ("g") ("B")?> | |
| | <IDENTIFIER: <LETTER> (<DIGIT>|<LETTER>)* > | |
| | <COLON: ":" > | |
| | <DASH: "-" > | |
| | <PLUS: "+" > | |
| | <DELIM: ("|"|";") > | |
| } | |
| public java.util.List<Segment> many(): | |
| { | |
| java.util.List<Segment> L=new java.util.ArrayList<Segment>(); | |
| Segment s1; | |
| Segment s2; | |
| } | |
| { | |
| ( (s1=segment() { L.add(s1);} ((<DELIM>)? s2=segment() { L.add(s2);} )* )? <EOF>) | |
| { | |
| return L; | |
| } | |
| } | |
| public Segment one():{Segment pos; } | |
| { | |
| ( pos=segment() <EOF>) | |
| { | |
| return pos; | |
| } | |
| } | |
| private Segment segment():{String chrom;BigInteger start=null; BigInteger end=null ; char sign='?';} | |
| { | |
| ( chrom=chromName() <COLON> start= position() (<DASH> end=position() {sign='-';}| <PLUS> end=position() {sign='+';})? ) | |
| { | |
| switch(sign) | |
| { | |
| case '?': end=start.add(BigInteger.ONE);break; | |
| case '-': break; | |
| case '+': start=start.subtract(end);end=BigInteger.ONE.add(start.add(end.multiply(TWO)));break; | |
| } | |
| if(start.compareTo(BigInteger.ZERO)<0) throw new ParseException(start.toString()+" < 0)"); | |
| if(end.compareTo(start)<0) throw new ParseException(start.toString()+" > "+end+")"); | |
| if(INT_MAX.compareTo(start)<=0) throw new ParseException(start.toString()+" > "+ INT_MAX); | |
| if(INT_MAX.compareTo(end)<=0) throw new ParseException(end.toString()+" > "+ INT_MAX); | |
| return new Segment(chrom,start.intValue(),end.intValue()); | |
| } | |
| } | |
| private BigInteger position():{BigInteger i=null; BigInteger mul=BigInteger.ONE;} | |
| { | |
| i=integer() (mul=factor())? { return i.multiply(mul);} | |
| } | |
| private BigInteger factor():{} | |
| { | |
| ( | |
| <BP> { return new BigInteger("1");} | |
| | <KB> { return new BigInteger("1000");} | |
| | <MB> { return new BigInteger("1000000");} | |
| | <GB> { return new BigInteger("1000000000");} | |
| ) | |
| } | |
| private BigInteger integer():{Token t;} | |
| { | |
| t=<INT> { return new BigInteger(t.image.replace(",","")); } | |
| } | |
| private String chromName():{BigInteger i; String s;} | |
| { | |
| ( i=integer() { return "chr"+i.toString(); } | |
| | s=identifier() { return s;} | |
| ) | |
| } | |
| private String identifier():{Token t;} | |
| { | |
| t=<IDENTIFIER> { return t.image; } | |
| } |
Compiling
javacc SegmentParser.jj
javac SegmentParser.java
javac SegmentParser.java
Running
echo " chrM:1-100,000"| java SegmentParser
chrM:1-100000
echo " c1:1000"| java SegmentParser
c1:1000-1001
echo "2:1Gb+1 " | java SegmentParser
chr2:999999999-1000000002
echo "chr2:10+100" | java SegmentParser
ParseException: -90 < 0)
echo "chrX:3147483647" | java SegmentParser
ParseException: 3147483647 > 2147483647 (int-max)
echo "2:1Gb+a azd " | java SegmentParser
ParseException: Encountered "a" at line 1, column 7
chrM:1-100000
echo " c1:1000"| java SegmentParser
c1:1000-1001
echo "2:1Gb+1 " | java SegmentParser
chr2:999999999-1000000002
echo "chr2:10+100" | java SegmentParser
ParseException: -90 < 0)
echo "chrX:3147483647" | java SegmentParser
ParseException: 3147483647 > 2147483647 (int-max)
echo "2:1Gb+a azd " | java SegmentParser
ParseException: Encountered "a" at line 1, column 7
That's it,
Pierre
