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towards wobbling long-period tandems
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| package de.mpi_cbg.revant.apps; | ||
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| import de.mpi_cbg.revant.util.IO; | ||
| import java.io.*; | ||
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| /** | ||
| * Like $Wobble.java$. | ||
| */ | ||
| public class WobbleLongPeriod { | ||
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| public static void main(String[] args) throws IOException { | ||
| final String TRANSLATED_READS_CHARACTERS_FILE = args[0]; // Of a chunk of reads | ||
| final int WOBBLE_LENGTH = Integer.parseInt(args[1]); | ||
| final String ALPHABET_FILE_OLD = args[2]; // Of all reads | ||
| final String ALPHABET_FILE_NEW = args[3]; // Of all reads | ||
| final String ALPHABET_FILE_OLD2NEW = args[4]; // Of all reads | ||
| final String REPEAT_LENGTHS_FILE = args[5]; | ||
| final int N_REPEATS = Integer.parseInt(args[6]); | ||
| final String TANDEMS_FILE = args[7]; // Of a chunk of reads. Non-periodic only. | ||
| final String OUTPUT_FILE = args[8]; // Of a chunk of reads | ||
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| int i; | ||
| int nBlocks, lastUnique_new, lastPeriodic_new, lastAlphabet_new; | ||
| String str1, str2; | ||
| BufferedReader br1, br2; | ||
| BufferedWriter bw; | ||
| int[] old2new, tmpArray1, tmpArray2, tmpArray3; | ||
| RepeatAlphabet.Character[] alphabet_new; | ||
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| RepeatAlphabet.loadRepeatLengths(REPEAT_LENGTHS_FILE,N_REPEATS); | ||
| RepeatAlphabet.deserializeAlphabet(ALPHABET_FILE_NEW,2); | ||
| alphabet_new=RepeatAlphabet.alphabet; lastUnique_new=RepeatAlphabet.lastUnique; lastPeriodic_new=RepeatAlphabet.lastPeriodic; lastAlphabet_new=RepeatAlphabet.lastAlphabet; | ||
| RepeatAlphabet.deserializeAlphabet(ALPHABET_FILE_OLD,2); | ||
| old2new = new int[lastAlphabet_new+1]; | ||
| br1 = new BufferedReader(new FileReader(ALPHABET_FILE_OLD2NEW)); | ||
| for (i=0; i<=RepeatAlphabet.lastAlphabet; i++) old2new[i]=Integer.parseInt(br1.readLine()); | ||
| br1.close(); | ||
| tmpArray1 = new int[100]; // Arbitrary | ||
| tmpArray2 = new int[RepeatAlphabet.lastAlphabet+1]; | ||
| tmpArray3 = new int[] {0,0}; | ||
| br1 = new BufferedReader(new FileReader(TRANSLATED_READS_CHARACTERS_FILE)); | ||
| br2 = new BufferedReader(new FileReader(TANDEMS_FILE)); | ||
| bw = new BufferedWriter(new FileWriter(OUTPUT_FILE)); | ||
| str1=br1.readLine(); str2=br2.readLine(); | ||
| while (str1!=null) { | ||
| nBlocks=1+((str1.length()+1)>>1); // Loose upper bound | ||
| if (tmpArray1.length<nBlocks) tmpArray1 = new int[nBlocks]; | ||
| RepeatAlphabet.wobble_longPeriod(str1,str2,WOBBLE_LENGTH,IO.quantum,old2new,alphabet_new,lastUnique_new,lastPeriodic_new,lastAlphabet_new,bw,tmpArray1,tmpArray2,tmpArray3); | ||
| str1=br1.readLine(); str2=br2.readLine(); | ||
| } | ||
| br1.close(); br2.close(); bw.close(); | ||
| System.err.println("Applied wobbling to "+tmpArray3[0]+" blocks out of "+tmpArray3[1]+" total ("+((100.0*tmpArray3[0])/tmpArray3[1])+"%)"); | ||
| } | ||
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| } |
58 changes: 58 additions & 0 deletions
58
src/de/mpi_cbg/revant/apps/WobbleLongPeriodCreateAlphabet1.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| package de.mpi_cbg.revant.apps; | ||
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| import de.mpi_cbg.revant.util.Math; | ||
| import de.mpi_cbg.revant.util.IO; | ||
| import java.io.*; | ||
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| /** | ||
| * Marks all characters of the alphabet that are adjacent to a long-period tandem or that | ||
| * belong to a long-period tandem in some translation, and prints the corresponding | ||
| * bitvector in output. | ||
| * | ||
| * This is designed to work on a chunk of reads. | ||
| */ | ||
| public class WobbleLongPeriodCreateAlphabet1 { | ||
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| public static void main(String[] args) throws IOException { | ||
| final String ALPHABET_FILE = args[0]; // Of all reads | ||
| final String TRANSLATED_READS_CHARACTERS_FILE = args[1]; // Of a chunk of reads | ||
| final String TANDEMS_FILE = args[2]; // Of a chunk of reads. Non-periodic only. | ||
| final String READ_LENGTHS_FILE = args[3]; // Of a chunk of reads | ||
| final String OUTPUT_FILE = args[4]; | ||
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| int i; | ||
| int nBlocks, nFlags; | ||
| String str1, str2, str3; | ||
| RepeatAlphabet.Character tmpCharacter; | ||
| BufferedReader br1, br2, br3; | ||
| BufferedWriter bw; | ||
| boolean[] flags; | ||
| int[] tmpArray; | ||
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| tmpCharacter = new RepeatAlphabet.Character(); | ||
| RepeatAlphabet.deserializeAlphabet(ALPHABET_FILE,2); | ||
| flags = new boolean[RepeatAlphabet.lastAlphabet+1]; | ||
| Math.set(flags,RepeatAlphabet.lastAlphabet,false); | ||
| if (RepeatAlphabet.lastAlphabet>RepeatAlphabet.lastPeriodic) { | ||
| tmpArray = new int[100]; // Arbitrary | ||
| br1 = new BufferedReader(new FileReader(TRANSLATED_READS_CHARACTERS_FILE)); | ||
| br2 = new BufferedReader(new FileReader(TANDEMS_FILE)); | ||
| br3 = new BufferedReader(new FileReader(READ_LENGTHS_FILE)); | ||
| str1=br1.readLine(); str2=br2.readLine(); str3=br3.readLine(); | ||
| i=0; | ||
| while (str1!=null) { | ||
| nBlocks=1+((str1.length()+1)>>1); // Loose upper bound | ||
| if (tmpArray.length<nBlocks) tmpArray = new int[nBlocks]; | ||
| RepeatAlphabet.wobble_longPeriod_markAlphabet(str1,str2,Integer.parseInt(str3),flags,tmpCharacter,tmpArray); | ||
| i++; | ||
| if (i%10000==0) System.err.println("Processed "+i+" reads"); | ||
| str1=br1.readLine(); str2=br2.readLine(); str3=br3.readLine(); | ||
| } | ||
| br1.close(); br2.close(); br3.close(); | ||
| } | ||
| bw = new BufferedWriter(new FileWriter(OUTPUT_FILE)); | ||
| for (i=0; i<=RepeatAlphabet.lastAlphabet; i++) bw.write(flags[i]?"1\n":"0\n"); | ||
| bw.close(); | ||
| } | ||
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| } |