broad.core.multiplealignment.AlignmentExtractor Class Reference

Collaboration diagram for broad.core.multiplealignment.AlignmentExtractor:

Static Public Member Functions
static void	main (String[] args) throws IOException, IllegalAccessException, ParseException
static void	extractGFFRegions (String alignmentFile, String outputFile, String gff, String inFormat, String outFormat, String[] seqs) throws IOException, ParseException

Static Public Attributes
static ArrayList< String >	degenerateCodonStarts
static ArrayList< String >	twoFoldDegenerateCodons
static ArrayList< String >	threeFoldDegenerateCodons
static ArrayList< String >	nonDegenerateCodons
static HashMap< String, String >	codonToAminoacid
static String	USAGE

Member Function Documentation

static void broad.core.multiplealignment.AlignmentExtractor.extractGFFRegions ( String  alignmentFile, String  outputFile, String  gff, String  inFormat, String  outFormat, String[]  seqs  ) throws IOException, ParseException

static

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static void broad.core.multiplealignment.AlignmentExtractor.main ( String[]  args ) throws IOException, IllegalAccessException, ParseException

static

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Member Data Documentation

HashMap<String, String> broad.core.multiplealignment.AlignmentExtractor.codonToAminoacid

static

ArrayList<String> broad.core.multiplealignment.AlignmentExtractor.degenerateCodonStarts

static

ArrayList<String> broad.core.multiplealignment.AlignmentExtractor.nonDegenerateCodons

static

ArrayList<String> broad.core.multiplealignment.AlignmentExtractor.threeFoldDegenerateCodons

static

ArrayList<String> broad.core.multiplealignment.AlignmentExtractor.twoFoldDegenerateCodons

static

String broad.core.multiplealignment.AlignmentExtractor.USAGE

static

Initial value:

= "Usage: AlignmentExtractor TASK=<task_num> <task_args>\n" +
    "\tTasks:\n" +
    "\t\t1. Extract Regions: IN=<Multiple alignment file> OUT=<output file> ANNOTGFF=<GFF annotation file, sequence name should match one of the aligned sequence IDs> INFORMAT=<[FASTA]/EXON/PHYLIP/SEQPHYLIP> OUTFORMAT<[FASTA]/EXON/PHYLIP> SEQS=<comma separated list of sequence ids>\n" +
    "\t\t2. Extract 4D sites from exon alignment: IN=<Exon multiple alignment> OUT=<output file> INFORMAT=<input format (default FASTA)> OUTFORMAT=<output format (default FASTA)>\n " +
    "\t\t3. Extract Conserved sites from exon alignment: IN=<Exon multiple alignment> OUT=<output alignment file> INFORMAT=<input format (default FASTA)> OUTFORMAT=<output format (default FASTA)>\n"+
    "\t\t4. Extract region IN=<Multiple alignment file> OUT=<output file> REGION=<start..end> REF=<reference> INFORMAT=<[FASTA]/EXON/PHYLIP> OUTFORMAT<[FASTA]/EXON/PHYLIP/SEQPHYLIP> \n" +
    "\t\t5. Convert alignment file IN=<Multiple Alignment File> OUT=<output file> INFORMAT=<[FASTA]/EXON/PHYLIP> OUTFORMAT<FASTA/EXON/[PHYLIP]/SEQPHYLIP> [-compress <if the output alignment should be reference gap free>] \n" +
    "\t\t6. Introduce Random Gaps -in <Multiple Alignment File default is standard input> -out <output gapped alignment defalut is standard out> -informat <[FASTA]/EXON/PHYLIP> -outformat <FASTA/EXON/[PHYLIP]/SEQPHYLIP> -maxGaps <maximum number of gaps> [-ref <reference if no gaps should be introduced in reference>]\n" +
    "\t\t7. Permute Columns -in <Multiple Alignment File default is standard input> -out <output gapped alignment defalut is standard out> -informat <[FASTA]/EXON/PHYLIP> -outformat <FASTA/EXON/[PHYLIP]/SEQPHYLIP> " +
    "\n\t8. Sample Columns from Alignment -in <Multiple Alignment File default is standard input> -out <output gapped alignment defalut is standard out> -informat <[FASTA]/EXON/PHYLIP> -outformat <[FASTA]/EXON/PHYLIP/SEQPHYLIP> -cols <Number of columns to sample> [-consecutiveCols <Sample consecutive columns rather than single ones>]" +
    "\n\t9. Combined alignments -informat <[FASTA], PHYLIP, SEQPHYLIP> -outformat <[FASTA], PHYLIP, SEQPHYLIP> -in <Standard input of file with a list of alignment files> -out <standard output or file name> [-maxColumns <If specified, and the combined alignment is larger than this value, a sampled alignmnet will be generated instead of the combined one>]" +
    "\n"

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

• java/broad/core/multiplealignment/AlignmentExtractor.java