edu.mssm.crover.tools.tissue
Class tiambiguity

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

public class tiambiguity

extends java.lang.Object

Constructor Summary

tiambiguity()

Method Summary

static java.lang.String[]	getAcc(java.lang.String[] args)
static java.lang.String	getAccsFile(java.lang.String[] args) Returns the name of the file with the list of accession numbers.
static java.lang.String	getCacheFile(java.lang.String[] args) Returns the name of the file into which the cache is to be serialized.
static java.lang.String	getIEIFile(java.lang.String[] args) Returns the name of the file with the list of tissues that the gene expression is to be tested against.
static java.lang.String	getISTFile(java.lang.String[] args) Returns the name of the file with the list of tissues that the gene expression specificity is to be tested against.
static java.lang.String	getOutFile(java.lang.String[] args) Sets the prefix for the result files.
static double	getPurity(java.lang.String[] args) Returns the sequencing error rate.
static java.lang.String	getTiacFile(java.lang.String[] args) Returns the name of the query sequence input file.
static java.lang.String	getTiacsFile(java.lang.String[] args) Returns the name of the file which lists the tiac files to be queried.
static void	main(java.lang.String[] args)
static void	printHelpFile()

Methods inherited from class java.lang.Object

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

Constructor Detail

tiambiguity

public tiambiguity()

Method Detail

getTiacFile

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

Returns the name of the query sequence input file. Read from the command line, after "-tiac" flag. This, or -tiacs, is a necessary parameter.

getTiacsFile

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

Returns the name of the file which lists the tiac files to be queried. Read from the command line, after "-tiacs" flag. This, or -tiac, is a necessary parameter.

getOutFile

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

Sets the prefix for the result files. If no output file name is specified, the default prefix is "tiquery".

getPurity

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

Returns the sequencing error rate. If there is no error rate specified on the command line, a default of 95% is used.

getAccsFile

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

Returns the name of the file with the list of accession numbers. Read from the command line, after "-accs" flag.

getAcc

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

getISTFile

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

Returns the name of the file with the list of tissues that the gene expression specificity is to be tested against. Read from the command line, after "-isSpecificToFile" flag.

getIEIFile

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

Returns the name of the file with the list of tissues that the gene expression is to be tested against. Read from the command line, after "-isExpressedInFile" flag.

getCacheFile

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

Returns the name of the file into which the cache is to be serialized. Read from the command line, after "-ser" flag.

printHelpFile

public static void printHelpFile()

main

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