/*
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.tools.biostar;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.io.Reader;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.util.bio.AcidNucleics;
import com.github.lindenb.jvarkit.util.bio.Rebase;
import com.github.lindenb.jvarkit.util.jcommander.Launcher;
import com.github.lindenb.jvarkit.util.jcommander.Program;
import com.github.lindenb.jvarkit.util.log.Logger;
/**
BEGIN_DOC
## Example
```bash
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr3.fa.gz" |\
gunzip -c |\
java -jar dist/biostar86480.jar -E AarI -E EcoRI
chr3 60645 60651 GAATTC 1000 + EcoRI G^AATTC
chr3 60953 60959 GAATTC 1000 + EcoRI G^AATTC
chr3 68165 68172 GCAGGTG 1000 - AarI CACCTGC(4/8)
chr3 70263 70269 GAATTC 1000 + EcoRI G^AATTC
chr3 70945 70952 GCAGGTG 1000 - AarI CACCTGC(4/8)
chr3 71140 71146 GAATTC 1000 + EcoRI G^AATTC
chr3 72264 72270 GAATTC 1000 + EcoRI G^AATTC
chr3 74150 74156 GAATTC 1000 + EcoRI G^AATTC
chr3 75063 75069 GAATTC 1000 + EcoRI G^AATTC
chr3 78438 78444 GAATTC 1000 + EcoRI G^AATTC
chr3 81052 81059 CACCTGC 1000 + AarI CACCTGC(4/8)
chr3 84498 84504 GAATTC 1000 + EcoRI G^AATTC
chr3 84546 84552 GAATTC 1000 + EcoRI G^AATTC
chr3 84780 84787 CACCTGC 1000 + AarI CACCTGC(4/8)
chr3 87771 87777 GAATTC 1000 + EcoRI G^AATTC
chr3 95344 95351 GCAGGTG 1000 - AarI CACCTGC(4/8)
chr3 96358 96364 GAATTC 1000 + EcoRI G^AATTC
chr3 96734 96740 GAATTC 1000 + EcoRI G^AATTC
chr3 105956 105962 GAATTC 1000 + EcoRI G^AATTC
chr3 107451 107457 GAATTC 1000 + EcoRI G^AATTC
(...)
```
END_DOC
*/
@Program(name="biostar86480",description="Genomic restriction finder",biostars=86480,
keywords={"rebase","genome","enzyme","restricion","genome"})
public class Biostar86480 extends Launcher
{
private static final Logger LOG = Logger.build(Biostar86480.class).make();
@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
private File outputFile = null;
@Parameter(names={"-E","--enzyme"},description="restrict to that enzyme.")
private Set<String> onlyEnz = new HashSet<>();
private Rebase rebase=Rebase.createDefaultRebase();
private Biostar86480()
{
}
private void digest(
String seqName,
int position0,
final List<Character> sequence,
PrintStream out
)
{
for(Rebase.Enzyme enzyme:this.rebase)
{
if(enzyme.size()>sequence.size()) continue;
for(int strand=0;strand<2;++strand)
{
int x=0;
for(x=0;x< enzyme.size();++x)
{
char c=(strand==0?
enzyme.at(x):
AcidNucleics.complement(enzyme.at((enzyme.size()-1)-x))
);
if(!Rebase.compatible(sequence.get(x),c)) break;
}
if(x==enzyme.size())
{
out.print(seqName);
out.print('\t');
out.print(position0);
out.print('\t');
out.print(position0+enzyme.size());
out.print('\t');
for(int y=0;y< enzyme.size();++y)
{
out.print(sequence.get(y));
}
out.print('\t');
out.print(1000);
out.print('\t');
out.print(strand==1?'-':'+');
out.print('\t');
out.print(enzyme.getName());
out.print('\t');
out.print(enzyme.getDecl());
out.println();
break;
}
if(enzyme.isPalindromic()) break;
}
}
}
private void run(Reader in,PrintStream out) throws IOException
{
int longest=0;
for(Rebase.Enzyme E:this.rebase)
{
longest=Math.max(E.size(), longest);
}
String seqName="";
int position0=0;
ArrayList<Character> sequences=new ArrayList<Character>(longest);
for(;;)
{
int c=in.read();
if(c==-1 || c=='>')
{
while(!sequences.isEmpty())
{
digest(seqName,position0,sequences,out);
++position0;
sequences.remove(0);
}
if(c==-1) break;
StringBuilder b=new StringBuilder();
while((c=in.read())!=-1 && c!='\n')
{
b.append((char)c);
}
seqName=b.toString();
position0=0;
}
else if(!Character.isWhitespace(c))
{
sequences.add((char)Character.toUpperCase(c));
if(sequences.size()==longest)
{
digest(seqName,position0,sequences,out);
++position0;
sequences.remove(0);
if(position0%1000000==0)
{
LOG.info(seqName+" "+position0);
}
}
}
}
}
@Override
public int doWork(List<String> args) {
if(!onlyEnz.isEmpty())
{
Rebase rebase2=new Rebase();
for(String e:onlyEnz)
{
Rebase.Enzyme enz=this.rebase.getEnzymeByName(e);
if(enz==null)
{
System.err.println("Cannot find enzyme "+enz +" in RE list.");
System.err.println("Current list is:");
for(Rebase.Enzyme E: this.rebase)
{
System.err.println("\t"+E);
}
return -1;
}
rebase2.getEnzymes().add(enz);
}
this.rebase=rebase2;
}
PrintStream out;
try
{
out = super.openFileOrStdoutAsPrintStream(this.outputFile);
if(args.isEmpty())
{
LOG.info("Reading from stdin");
run(new InputStreamReader(stdin()),out);
}
else
{
for(String arg:args)
{
LOG.info("Opening "+arg);
final Reader in=IOUtils.openURIForBufferedReading(arg);
run(in,out);
in.close();
}
}
out.flush();
out.close();
return 0;
}
catch(final Throwable err)
{
LOG.error(err);
return -1;
}
}
/**
* @param args
*/
public static void main(String[] args)
{
new Biostar86480().instanceMainWithExit(args);
}
}