Rebase.java

/*
The MIT License (MIT)

Copyright (c) 2014 Pierre Lindenbaum

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.


History:
* 2014 creation

*/
package com.github.lindenb.jvarkit.util.bio;

import java.util.AbstractList;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;

/**
 * Restriction Enzyme Database
 * @author lindenb
 *
 */
public class Rebase
	extends AbstractList<Rebase.Enzyme>
	implements Iterable<Rebase.Enzyme>
	{
	private final List<Rebase.Enzyme> enzymes=new ArrayList<Rebase.Enzyme>();
	public interface Enzyme
		{
		public String getName();
		public String getDecl();
		public String getBases();
		public boolean isPalindromic();
		public int size();
		public char at(int index);
		public float getWeight();
		}
	
	public  Rebase.Enzyme getEnzymeByName(final String name)
		{
		return this.stream().
			filter(F->F.getName().equals(name)).
			findFirst().orElse(null);
		}
	
	@Override 
	public Rebase.Enzyme get(final int index)
		{
		return getEnzymes().get(index);
		}
	
	@Override 
	public int size()
		{
		return getEnzymes().size();
		}
	
	public List<Rebase.Enzyme> getEnzymes()
		{
		return enzymes;
		}
	
	@Override
	public Iterator<Enzyme> iterator()
		{
		return getEnzymes().iterator();
		}
	
	/**
	 * compatible
	 * @param plasmid seq from REF
	 * @param enzyme char from ENZ
	 * @return
	 */
	public static boolean compatible(
			char plasmid,
			char enzyme
			)
		{
		switch(plasmid)
			{
			case 'A': case 'a' : return "ANDHVMWR".indexOf(enzyme)!=-1;
            case 'T': case 't' : return "TNYBDHKW".indexOf(enzyme)!=-1;
            case 'G': case 'g' : return "GNRBDVKS".indexOf(enzyme)!=-1;
            case 'C': case 'c' : return "CNYBHVMS".indexOf(enzyme)!=-1;
            case 'N': case 'n' : return false;
			default: return false;
			}
		}

	
	
	public class EnzymeImpl implements Enzyme
		{
		private final String name;
		private final String seq;
		private final String decl;
		private final boolean palindromic;
		private float weight=0f;
		public EnzymeImpl(final String name,final String decl)
			{
			this.name=name;
			this.decl=decl;
			this.seq=decl.replaceAll("[^A-Za-z]","").toUpperCase();
			this.palindromic=decl.contains("^");
			for(int i=0;i< this.seq.length();++i)
				{
				this.weight+=AcidNucleics.weight(this.seq.charAt(i));
				}	
			}
		public float getWeight() { return this.weight;}
		public String getName() { return this.name;}
		public String getBases() { return this.seq;}
		public String getDecl() { return this.decl;}
		public int size() { return this.seq.length();}
		public boolean isPalindromic() { return this.palindromic;}
		public char at(int index) { return this.seq.charAt(index); }
		@Override
		public boolean equals(final Object obj)
			{
			if(this==obj) return true;
			if(obj==null || !(obj instanceof EnzymeImpl)) return false;
			return EnzymeImpl.class.cast(obj).name.equals(this.name);
			}
		@Override
		public int hashCode()
			{
			return name.hashCode();
			}
		
		@Override
		public String toString()
			{
			return name+"["+decl+"]";
			}
		}
	
	private void add(final String name,final String decl)
		{
		this.enzymes.add(new EnzymeImpl(name, decl));
		}
	
	/** Neoschizomers are restriction enzymes that recognize the same nucleotide sequence as their prototype but cleave at a different site. */
	public Rebase removeNeoschizomers()
		{
		final Set<String> seen = new HashSet<>();
		int i=0;
		while(i< this.enzymes.size())
			{
			final Enzyme e = this.enzymes.get(i);
			if(!seen.add(e.getBases()))
				{
				this.enzymes.remove(i);
				}
			else
				{
				i++;
				}
			}
		return this;
		}
	
	public static Rebase createDefaultRebase()
		{
		final Rebase rebase=new Rebase();
		/* curl -s "ftp://ftp.neb.com/pub/rebase/allenz.txt" |grep -E '^<[1257]>' | awk '/^<[^7]>/ {printf("%s\t",substr($0,4)); next;} /^<7>/ {print substr($0,4); next;}' | awk -F '       ' '($2=="" && $3!="?" && $4!="?" && $4!="")'  | cut  -f 1,3 | sort -k1,1 | awk '{printf("rebase.add(\"%s\",\"%s\");\n",$1,$2);}' */
		rebase.add("AarI","CACCTGC(4/8)");
		rebase.add("AatII","GACGT^C");
		rebase.add("AbsI","CC^TCGAGG");
		rebase.add("AccI","GT^MKAC");
		rebase.add("AciI","CCGC(-3/-1)");
		rebase.add("AclI","AA^CGTT");
		rebase.add("AcyI","GR^CGYC");
		rebase.add("AflII","C^TTAAG");
		rebase.add("AflIII","A^CRYGT");
		rebase.add("AgeI","A^CCGGT");
		rebase.add("AgsI","TTS^AA");
		rebase.add("AjuI","(7/12)GAANNNNNNNTTGG(11/6)");
		rebase.add("AlfI","(10/12)GCANNNNNNTGC(12/10)");
		rebase.add("AloI","(7/12)GAACNNNNNNTCC(12/7)");
		rebase.add("AluI","AG^CT");
		rebase.add("AlwNI","CAGNNN^CTG");
		rebase.add("ApaI","GGGCC^C");
		rebase.add("ApaLI","G^TGCAC");
		rebase.add("ApoI","R^AATTY");
		rebase.add("ArsI","(8/13)GACNNNNNNTTYG(11/6)");
		rebase.add("AscI","GG^CGCGCC");
		rebase.add("AsuII","TT^CGAA");
		rebase.add("AvaI","C^YCGRG");
		rebase.add("AvaII","G^GWCC");
		rebase.add("AvrII","C^CTAGG");
		rebase.add("BaeI","(10/15)ACNNNNGTAYC(12/7)");
		rebase.add("BalI","TGG^CCA");
		rebase.add("BamHI","G^GATCC");
		rebase.add("BarI","(7/12)GAAGNNNNNNTAC(12/7)");
		rebase.add("BbvCI","CCTCAGC(-5/-2)");
		rebase.add("BbvI","GCAGC(8/12)");
		rebase.add("BccI","CCATC(4/5)");
		rebase.add("BcgI","(10/12)CGANNNNNNTGC(12/10)");
		rebase.add("BciVI","GTATCC(6/5)");
		rebase.add("BclI","T^GATCA");
		rebase.add("BglI","GCCNNNN^NGGC");
		rebase.add("BglII","A^GATCT");
		rebase.add("BisI","GC^NGC");
		rebase.add("BplI","(8/13)GAGNNNNNCTC(13/8)");
		rebase.add("Bpu10I","CCTNAGC(-5/-2)");
		rebase.add("BsaAI","YAC^GTR");
		rebase.add("BsaBI","GATNN^NNATC");
		rebase.add("BsaXI","(9/12)ACNNNNNCTCC(10/7)");
		rebase.add("BseMII","CTCAG(10/8)");
		rebase.add("BsePI","G^CGCGC");
		rebase.add("BseRI","GAGGAG(10/8)");
		rebase.add("BseSI","GKGCM^C");
		rebase.add("BseYI","CCCAGC(-5/-1)");
		rebase.add("BsgI","GTGCAG(16/14)");
		rebase.add("BsmAI","GTCTC(1/5)");
		rebase.add("BsmI","GAATGC(1/-1)");
		rebase.add("Bsp1407I","T^GTACA");
		rebase.add("BspHI","T^CATGA");
		rebase.add("BspMI","ACCTGC(4/8)");
		rebase.add("BsrBI","CCGCTC(-3/-3)");
		rebase.add("BsrDI","GCAATG(2/0)");
		rebase.add("BsrI","ACTGG(1/-1)");
		rebase.add("BstEII","G^GTNACC");
		rebase.add("BstXI","CCANNNNN^NTGG");
		rebase.add("BtgZI","GCGATG(10/14)");
		rebase.add("BtrI","CACGTC(-3/-3)");
		rebase.add("BtsI","GCAGTG(2/0)");
		rebase.add("BtsIMutI","CAGTG(2/0)");
		rebase.add("Cac8I","GCN^NGC");
		rebase.add("Cfr10I","R^CCGGY");
		rebase.add("ClaI","AT^CGAT");
		rebase.add("CspCI","(11/13)CAANNNNNGTGG(12/10)");
		rebase.add("CviJI","RG^CY");
		rebase.add("DdeI","C^TNAG");
		rebase.add("DpnI","GA^TC");
		rebase.add("DraIII","CACNNN^GTG");
		rebase.add("DrdI","GACNNNN^NNGTC");
		rebase.add("Eam1105I","GACNNN^NNGTC");
		rebase.add("EciI","GGCGGA(11/9)");
		rebase.add("Eco31I","GGTCTC(1/5)");
		rebase.add("Eco47III","AGC^GCT");
		rebase.add("Eco57I","CTGAAG(16/14)");
		rebase.add("EcoNI","CCTNN^NNNAGG");
		rebase.add("EcoP15I","CAGCAG(25/27)");
		rebase.add("EcoRI","G^AATTC");
		rebase.add("EcoRII","^CCWGG");
		rebase.add("EcoRV","GAT^ATC");
		rebase.add("Esp3I","CGTCTC(1/5)");
		rebase.add("FaiI","YA^TR");
		rebase.add("FalI","(8/13)AAGNNNNNCTT(13/8)");
		rebase.add("FauI","CCCGC(4/6)");
		rebase.add("Fnu4HI","GC^NGC");
		rebase.add("FokI","GGATG(9/13)");
		rebase.add("FseI","GGCCGG^CC");
		rebase.add("FspAI","RTGC^GCAY");
		rebase.add("FspEI","CC(12/16)");
		rebase.add("GlaI","GC^GC");
		rebase.add("GsuI","CTGGAG(16/14)");
		rebase.add("HaeII","RGCGC^Y");
		rebase.add("HaeIII","GG^CC");
		rebase.add("HgaI","GACGC(5/10)");
		rebase.add("HhaI","GCG^C");
		rebase.add("HindII","GTY^RAC");
		rebase.add("HindIII","A^AGCTT");
		rebase.add("HinfI","G^ANTC");
		rebase.add("HpaI","GTT^AAC");
		rebase.add("HpaII","C^CGG");
		rebase.add("HphI","GGTGA(8/7)");
		rebase.add("Hpy188I","TCN^GA");
		rebase.add("Hpy99I","CGWCG^");
		rebase.add("KpnI","GGTAC^C");
		rebase.add("KroI","G^CCGGC");
		rebase.add("LpnPI","CCDG(10/14)");
		rebase.add("MaeI","C^TAG");
		rebase.add("MaeII","A^CGT");
		rebase.add("MaeIII","^GTNAC");
		rebase.add("MauBI","CG^CGCGCG");
		rebase.add("MboI","^GATC");
		rebase.add("MboII","GAAGA(8/7)");
		rebase.add("MfeI","C^AATTG");
		rebase.add("MluI","A^CGCGT");
		rebase.add("MmeI","TCCRAC(20/18)");
		rebase.add("MnlI","CCTC(7/6)");
		rebase.add("MseI","T^TAA");
		rebase.add("MslI","CAYNN^NNRTG");
		rebase.add("MspJI","CNNR(9/13)");
		rebase.add("MwoI","GCNNNNN^NNGC");
		rebase.add("NaeI","GCC^GGC");
		rebase.add("NarI","GG^CGCC");
		rebase.add("NcoI","C^CATGG");
		rebase.add("NdeI","CA^TATG");
		rebase.add("NheI","G^CTAGC");
		rebase.add("NlaIII","CATG^");
		rebase.add("NlaIV","GGN^NCC");
		rebase.add("NmeAIII","GCCGAG(21/19)");
		rebase.add("NotI","GC^GGCCGC");
		rebase.add("NruI","TCG^CGA");
		rebase.add("NspI","RCATG^Y");
		rebase.add("OliI","CACNN^NNGTG");
		rebase.add("PacI","TTAAT^TAA");
		rebase.add("PasI","CC^CWGGG");
		rebase.add("PcsI","WCGNNNN^NNNCGW");
		rebase.add("PflMI","CCANNNN^NTGG");
		rebase.add("PfoI","T^CCNGGA");
		rebase.add("PleI","GAGTC(4/5)");
		rebase.add("PmaCI","CAC^GTG");
		rebase.add("PmeI","GTTT^AAAC");
		rebase.add("PpuMI","RG^GWCCY");
		rebase.add("PshAI","GACNN^NNGTC");
		rebase.add("PsiI","TTA^TAA");
		rebase.add("PspXI","VC^TCGAGB");
		rebase.add("PsrI","(7/12)GAACNNNNNNTAC(12/7)");
		rebase.add("PstI","CTGCA^G");
		rebase.add("PvuI","CGAT^CG");
		rebase.add("PvuII","CAG^CTG");
		rebase.add("RsaI","GT^AC");
		rebase.add("RsrII","CG^GWCCG");
		rebase.add("SacI","GAGCT^C");
		rebase.add("SacII","CCGC^GG");
		rebase.add("SalI","G^TCGAC");
		rebase.add("SapI","GCTCTTC(1/4)");
		rebase.add("ScaI","AGT^ACT");
		rebase.add("ScrFI","CC^NGG");
		rebase.add("SduI","GDGCH^C");
		rebase.add("SetI","ASST^");
		rebase.add("SexAI","A^CCWGGT");
		rebase.add("SfaNI","GCATC(5/9)");
		rebase.add("SfiI","GGCCNNNN^NGGCC");
		rebase.add("SgeI","CNNGNNNNNNNNN^");
		rebase.add("SgfI","GCGAT^CGC");
		rebase.add("SgrAI","CR^CCGGYG");
		rebase.add("SgrDI","CG^TCGACG");
		rebase.add("SmaI","CCC^GGG");
		rebase.add("SmlI","C^TYRAG");
		rebase.add("SnaBI","TAC^GTA");
		rebase.add("SpeI","A^CTAGT");
		rebase.add("SphI","GCATG^C");
		rebase.add("Sse8387I","CCTGCA^GG");
		rebase.add("SspI","AAT^ATT");
		rebase.add("StuI","AGG^CCT");
		rebase.add("StyI","C^CWWGG");
		rebase.add("SwaI","ATTT^AAAT");
		rebase.add("TaqI","T^CGA");
		rebase.add("TaqII","GACCGA(11/9)");
		rebase.add("TatI","W^GTACW");
		rebase.add("TauI","GCSG^C");
		rebase.add("TfiI","G^AWTC");
		rebase.add("TseI","G^CWGC");
		rebase.add("Tsp45I","^GTSAC");
		rebase.add("TspDTI","ATGAA(11/9)");
		rebase.add("TspGWI","ACGGA(11/9)");
		rebase.add("TspRI","CASTGNN^");
		rebase.add("Tth111I","GACN^NNGTC");
		rebase.add("VspI","AT^TAAT");
		rebase.add("XbaI","T^CTAGA");
		rebase.add("XcmI","CCANNNNN^NNNNTGG");
		rebase.add("XhoI","C^TCGAG");
		rebase.add("XhoII","R^GATCY");
		rebase.add("XmnI","GAANN^NNTTC");
		return rebase;
		}
	}