meme
Class MemeParser

java.lang.Object
  meme.MemeParser

public class MemeParser

extends java.lang.Object

Parses meme output into MemeMotif objects and stores some generalize info re the meme run. Must supply the full command line to fire meme, use full paths for meme and the seq file.

Constructor Summary

MemeParser(java.lang.String cndLine)
For single processor meme

MemeParser(java.lang.String fullPathMeme, java.lang.String fullPathFile, java.lang.String memeParams)
For parallel processor meme on Sapo

Method Summary

java.lang.String[]	fireMeme(java.lang.String aCmd)
java.lang.String[]	fireMemeParallel(java.lang.String fullPathMeme, java.lang.String fullPathFile, java.lang.String memeParams, java.lang.String fullPathToTempDir) Fires meme using a shell script and qsub, checks every 15 sec to see if done, returns unparsed MEME output.
java.lang.String	getCmdLn()
MemeMotif[]	getMemeMotifs()
int	getNumMotifs()
java.lang.String	getParsedFileName()
void	parseMemeText(java.lang.String[] data)
static java.lang.String	reverseCompDNA(java.lang.String seq) takes DNA seq and reverse comps it ambiguous symbols OK.
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

MemeParser

public MemeParser(java.lang.String cndLine)

For single processor meme

MemeParser

public MemeParser(java.lang.String fullPathMeme,
                  java.lang.String fullPathFile,
                  java.lang.String memeParams)

For parallel processor meme on Sapo

Method Detail

reverseCompDNA

public static java.lang.String reverseCompDNA(java.lang.String seq)

takes DNA seq and reverse comps it ambiguous symbols OK. Will warn if it finds an unrecognized base. Works with ' GATCRYWSKMBDHVNX .- ' upper or lower case

toString

public java.lang.String toString()

parseMemeText

public void parseMemeText(java.lang.String[] data)

fireMeme

public java.lang.String[] fireMeme(java.lang.String aCmd)

fireMemeParallel

public java.lang.String[] fireMemeParallel(java.lang.String fullPathMeme,
                                           java.lang.String fullPathFile,
                                           java.lang.String memeParams,
                                           java.lang.String fullPathToTempDir)

Fires meme using a shell script and qsub, checks every 15 sec to see if done, returns unparsed MEME output. To be run on Sapo cluster.

Parameters:

fullPathMeme - full path to the MEME program /home/sapo/software/seqanal/motifs/meme/meme.3.0.4/bin/meme

fullPathFile - full path to the multi FASTA for MEME to run on /home/sapo/nix/parMeme/kr4truk

memeParams - flags and options for the meme program -nmotifs 10 -evt 0.1 -minw 4 -maxw 12 -mod zoops -dna -revcomp -text -nostatus

fullPathToTempDir - full path to a directory where temporary files will be written and then deleted.

getCmdLn

public java.lang.String getCmdLn()

getNumMotifs

public int getNumMotifs()

getMemeMotifs

public MemeMotif[] getMemeMotifs()

getParsedFileName

public java.lang.String getParsedFileName()