forester/java/src/org/forester/application/aaa.java

   1
   2 package org.forester.application;
   3
   4 import java.io.FileInputStream;
   5 import java.util.ArrayList;
   6 import java.util.Collections;
   7 import java.util.HashSet;
   8 import java.util.List;
   9 import java.util.Set;
  10 import java.util.regex.Matcher;
  11 import java.util.regex.Pattern;
  12
  13 import org.forester.io.parsers.FastaParser;
  14 import org.forester.sequence.Sequence;
  15 import org.forester.util.ForesterUtil;
  16
  17 public class aaa {
  18
  19     public final static Pattern GN_PATTERN    = Pattern.compile( "GN=(\\S+)\\s" );     //use w+ instead of S+ for more stringent setting.
  20     public final static Pattern RANGE_PATTERN = Pattern.compile( "\\[(\\d+-\\d+)\\]" ); //use w+ instead of S+ for more stringent setting.
  21
  22     public static void main( final String args[] ) {
  23         try {
  24             System.out.println( "STARTING..." );
  25             final List<Sequence> orig = FastaParser
  26                     .parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20_2.fasta" ) );
  27             final List<String> new_seqs = new ArrayList<String>();
  28             for( final Sequence seq : orig ) {
  29                 final Matcher matcher = GN_PATTERN.matcher( seq.getIdentifier() );
  30                 String gn = "";
  31                 if ( matcher.find() ) {
  32                     gn = matcher.group( 1 );
  33                 }
  34                 else {
  35                     System.out.println( "ERROR: no gene for: " + seq.getIdentifier() );
  36                     System.exit( -1 );
  37                 }
  38                 new_seqs.add( ">" + gn + "|" + seq.getIdentifier() + "\n" + seq.getMolecularSequenceAsString() );
  39             }
  40             final Set<String> gn_ra_set = new HashSet<String>();
  41             final Set<String> mol_seq_set = new HashSet<String>();
  42             Collections.sort( new_seqs );
  43             int unique_counter = 0;
  44             int duplicate_counter_gn_ra = 0;
  45             int duplicate_counter_mol_seq = 0;
  46             String prev_gn = "____";
  47             for( final String seq : new_seqs ) {
  48                 final Matcher matcher_ra = RANGE_PATTERN.matcher( seq );
  49                 final Matcher matcher_gn = GN_PATTERN.matcher( seq );
  50                 String range = "";
  51                 if ( matcher_ra.find() ) {
  52                     range = matcher_ra.group( 1 );
  53                 }
  54                 else {
  55                     System.out.println( "ERROR: no range for: " + seq );
  56                     System.exit( -1 );
  57                 }
  58                 matcher_gn.find();
  59                 final String gn = matcher_gn.group( 1 );
  60                 final String gn_ra = gn + "_" + range;
  61                 if ( !gn_ra_set.contains( gn_ra ) ) {
  62                     gn_ra_set.add( gn_ra );
  63                     final String mol_seq = seq.split( "\n" )[ 1 ];
  64                     if ( !mol_seq_set.contains( mol_seq ) ) {
  65                         mol_seq_set.add( mol_seq );
  66                         if ( prev_gn.equals( gn ) ) {
  67                             int count = same_protein_seqs.size();
  68                             if ( count == 1 ) {
  69                                 System.out.println( seq );
  70                             }
  71                             else {
  72                                 int c = 1;
  73                                 for( final String s : same_protein_seqs ) {
  74                                     System.out.println( new StringBuffer( s ).insert( s.indexOf( "|" ),
  75                                                                                       "__" + c + "_OF_" + count )
  76                                             .toString() );
  77                                     c++;
  78                                 }
  79                             }
  80                         }
  81                         prev_gn = gn;
  82                         System.out.println( seq );
  83                         unique_counter++;
  84                     }
  85                     else {
  86                         duplicate_counter_mol_seq++;
  87                     }
  88                 }
  89                 else {
  90                     duplicate_counter_gn_ra++;
  91                 }
  92             }
  93             System.out.println( "unique   : " + unique_counter );
  94             System.out.println( "duplicate because gn and range same: " + duplicate_counter_gn_ra );
  95             System.out.println( "duplicate because mol seq same     : " + duplicate_counter_mol_seq );
  96         }
  97         catch ( final Exception e ) {
  98             e.printStackTrace();
  99         }
 100     }
 101 }