edu.mssm.crover.tools.tissue
Class timegablast

java.lang.Object
  |
  +--edu.mssm.crover.tools.tissue.timegablast

public class timegablast

extends java.lang.Object

Converts megablast output type 3 (-D 3) to tiac format. Keeps only matches with significant sequence identity (less than 5% error).

Constructor Summary

timegablast()

Method Summary

static java.lang.String	getAC(java.lang.String defline)
static boolean	getAssembleHsps(java.lang.String[] args) Returns true when hsps must be accumulated into hits of longer alignment length.
static java.lang.String	getDatabase(java.lang.String[] args) Returns the database name.
static double	getEValue(java.lang.String[] args) Returns the expectation value.
static float	getMaxError(java.lang.String[] args) Returns the maximum percentage of errors due to sequencing that is tolerated.
static java.lang.String	getMegaBlastFilename(java.lang.String[] args) Returns the name of the mega blast output file.
static java.lang.String	getOutFilename(java.lang.String[] args) Returns the name of the file in which to output accession numbers.
static int	getRequiredLength(java.lang.String[] args) Returns the minimal length required for an HSP to be considered as a hit.
static void	main(java.lang.String[] args)
static void	mbToTiac(java.lang.String mbFile, java.lang.String database, java.lang.String outFile, double eValue, float max_error, int required_length, boolean assemble_hsps)
static void	mbToTiac(java.lang.String mbFile, java.lang.String database, java.lang.String outFile, double eValue, float max_error, int required_length, boolean assemble_hsps, boolean exit)
static void	printHelp()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

timegablast

public timegablast()

Method Detail

getDatabase

public static java.lang.String getDatabase(java.lang.String[] args)

Returns the database name. Read from the command line, after "-db" flag.

getEValue

public static double getEValue(java.lang.String[] args)

Returns the expectation value. Read from the command line, after "-e" flag.

getMaxError

public static float getMaxError(java.lang.String[] args)

Returns the maximum percentage of errors due to sequencing that is tolerated. Read from the command line, after "-error" flag.

getRequiredLength

public static int getRequiredLength(java.lang.String[] args)

Returns the minimal length required for an HSP to be considered as a hit. Read from the command line, after "-required-length" flag.

getAssembleHsps

public static boolean getAssembleHsps(java.lang.String[] args)

Returns true when hsps must be accumulated into hits of longer alignment length. Read from the command line, after "-assemble-hsps" flag.

getMegaBlastFilename

public static java.lang.String getMegaBlastFilename(java.lang.String[] args)

Returns the name of the mega blast output file. Read from the command line, after "-mb" flag.

getOutFilename

public static java.lang.String getOutFilename(java.lang.String[] args)

Returns the name of the file in which to output accession numbers. Read from the command l ine, after "-tiac". If no output file name given, output file will be named "tiac.tiac".

printHelp

public static void printHelp()

main

public static void main(java.lang.String[] args)

mbToTiac

public static void mbToTiac(java.lang.String mbFile,
                            java.lang.String database,
                            java.lang.String outFile,
                            double eValue,
                            float max_error,
                            int required_length,
                            boolean assemble_hsps)

mbToTiac

public static void mbToTiac(java.lang.String mbFile,
                            java.lang.String database,
                            java.lang.String outFile,
                            double eValue,
                            float max_error,
                            int required_length,
                            boolean assemble_hsps,
                            boolean exit)

Parameters:

exit - Should be true if it's okay to do a System.exit(0), false if using TaskManagement, default = true Necessary to avoid the System.exit(0) which has to be taken out because in TaskManagement (TIWebUpdateScheduler), this breaks the pipeline.

getAC

public static java.lang.String getAC(java.lang.String defline)