broad.core.sequence.Extractor Class Reference

Public Member Functions
	Extractor ()

Static Public Member Functions
static void	main (String[] args) throws Exception

Static Public Attributes
static String	USAGE

Constructor & Destructor Documentation

broad.core.sequence.Extractor.Extractor

(

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Member Function Documentation

static void broad.core.sequence.Extractor.main ( String[]  args ) throws Exception

static

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Member Data Documentation

String broad.core.sequence.Extractor.USAGE

static

Initial value:

= "Usage: Extractor TASK=<task_num> <task_args>\n" +
    "\tTasks:\n" +
    "\t\t1. Batch Extract: IN=sequence id list file SEQ=sequence file OUT=output file\n" +
    "\t\t2. Extract Regions: IN=sequence file OUT=output file REGIONS=start1..end1,start2..end2.... SEQID=sequence id if multifasta(use -eq- for = and -s- for spaces REVERSE=Y/N\n UPPERCASE=<Y to uppercase all letters>\n" +
    "\t\t3. Extract records: -in <sequence file> -out <outout file> -seqids <seqId1,seqId2,seqId3,...> -reverse\n" +
    "\t\t4. Extract and Chunk: IN=<sequence file> PREFIX=<output file prefix> CHUNKSIZE=<chunk size> OVERLAP=<chunk overlap> REGION=start1..end1 SEQID=sequence id if multifasta(use -eq- for = and -s- for spaces and -lp- parenthesis and -rp- for right parenthesis> REVERSE=<Y/N> UPPERCASE=<Y to uppercase all letters>\n" +
    "\t\t5. Extract GC percent of all sequences in a multifasta file: IN=<sequence file>\n" +
    "\t\t6. Unchunk Fasta chunks: INDIR=<Directory with sequence chunks it assumes chunks files are named seqname_chunkStart_chunkEnd.extension (specify file extension with the EXT parameter) > \n"+
    "\t\t EXT=<chunk file extension> CHUNKSIZE=<chunk size> OVERLAP=<chunk overlap NOT HANDLING THIS YET>\n" +
    "\t\t7. Extract records matching motif in reverse or direct strand -in <multifasta file> -motif <sequence motif> -out <output file name>\n" +
    "\t\t8. Extract records with vClip preset parameters -in <multifasta>\n" +
    "\t\t9. Extract GC percent for the specified window size: -in <sequence file> -out <GC percent outout file> -windowSize <window size>\n" +
    "\t\t10. Reverse complement sequences in file: -in <sequence file or standard input> -out <file to output reverse-complemented sequences>" +
    "\n\t\t11. Extract sequences that are of at least the given length: -in <sequence file or standard input> -out <file to output or standard out> + -minLength <Minumum length of sequences to return>" +
    "\n\\t\t12. Extract sequences with names matching regular expression -in <sequence file or standard input> -out <file to output or standard out> -pattern <regex patterh>" +
    "\n"

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The documentation for this class was generated from the following file:

• java/broad/core/sequence/Extractor.java