HappyDoc Generated Documentation Class: Commandline

mabslib / Commandline.py / Commandline 

This is a command line based user interface.

The mabs commands and most of the default values are set here.

Base Classes   

Commandline
  Interface

Methods   
  printMatrices 
printMatrices ( self,  arglist )

Arguments: none prints the matrices

  isCommand 
isCommand ( self,  command )
  savematch 
savematch ( self,  arglist )

Arguments: [filename] saves the results of the matching in gff format See http://www.sanger.ac.uk/Software/formats/GFF/ The default filename is mabs_[Date+Time].gff e.g. mabs_2003_8_27_15_48.gff

  run 
run ( self )

waits for std input and executes these commands

  help 
help ( self,  arglist )

Arguments: none prints this help

  saveMarkovBackground 
saveMarkovBackground ( self,  arglist=None )

Arguments: filename Name of the file where to store the background model.

  savealign 
savealign ( self,  arglist )

Arguments: [filename] saves the alignment to disk The default filename is mabs_[Date+Time].align e.g. mabs_2003_9_16_11_48.align

  addSequence 
addSequence ( self,  arglist )

Arguments: filelist reads sequences from files

  setMarkovBG 
setMarkovBG ( self,  arglist=None )

Arguments: bgSampleSequence [order] Background sample sequence and order of the model or saved background file.

  getTFBSabsolute 
getTFBSabsolute ( self,  arglist )

Arguments: [cutoff] computes the scores of all matrices and all sequences which are better than cutoff. The default value for cutoff is 9.0

  setPseudoCnt 
setPseudoCnt ( self,  arglist=( "1.0" ) )

Arguments: [pseudocount] Set the amount of pseudocounts on matricies. Default 1.0

  setBGFreq 
setBGFreq ( self,  arglist=None )

Arguments: A C G T Background nucleotide frequencies. Removes markov background.

  removeMatrix 
removeMatrix ( self,  arglist )

Arguments: Matrixnumber removes a matrix

  resetMatrices 
resetMatrices ( self,  arglist )

Arguments: none removes all matrices

  printSeqNames 
printSeqNames ( self,  arglist )

Arguments: none prints the names of the sequences

  __init__ 
__init__ ( self )
  savealignGFF 
savealignGFF ( self,  arglist )

Arguments: [filename] saves the alignment to disk in GFF format The default filename is mabs_[Date+Time]_align.gff e.g. mabs_2003_9_16_11_48_align.gff

  reset 
reset ( self,  arglist )

Arguments: none removes all matrices and sequences

  quit 
quit ( self,  arglist )

Arguments: none to exit the program

  execute 
execute ( self,  command )

executes the given command (like run does)

  printMatrixWeights 
printMatrixWeights ( self,  arglist )

Arguments: none prints the matrix weights (with background)

  savealignAnchor 
savealignAnchor ( self,  arglist )

Arguments: [filename] saves the alignment to disk in Anchor format for DIALIGN The default filename is mabs_[Date+Time]_align.anc e.g. mabs_2003_9_16_11_48_align.anc

  removeSequence 
removeSequence ( self,  arglist )

Arguments: Sequencename removes a sequence

  align 
align ( self,  arglist )

Arguments: [filename[,num_of_align,[lambda[,xi[,mu[,nu,[,nuc_per_rotation]]]]]]] aligns the computed BS or optional the BS from a gff file filename specifies a file in gff format is you want to be aligned num_of_align specifies how many alignments you want. (Default 3) lambda Bonus factor for hit (Default 2) xi Penalty factor for rotation (Default 1.0) mu Penalty factor for average distance between sites (Default 0.5) nu Penalty factor for distance difference between sites (Default 1.0) nuc_per_rotation specifies how many nucletides there are per rotation. (Default 10.4) If you want to skip a argument just write '. for it. If you use .' as filename the local data are aligned.

  addMatrix 
addMatrix ( self,  arglist )

Arguments: filelist reads matrices from files

  getTFBS 
getTFBS ( self,  arglist )

Arguments: [bound] computes the scores of all matrices and all sequences which are better than bound*maxscore. maxscore is the highest reachable score of the actual matrix with respect to the background The default value for bound is 0.1

  resetSequences 
resetSequences ( self,  arglist )

Arguments: none removes all sequences

  showmatch 
showmatch ( self,  arglist )

Arguments: none prints the computed scores to stdout

  moreAlignment 
moreAlignment ( self,  arglist=( 1, ) )

Arguments: [number of alignments] prints more alignments from previously run alignment matrix

  about 
about ( self,  arglist )

Arguments: none Prints Information about the program

  addSingleSequence 
addSingleSequence ( self,  arglist )

Arguments: filelist Gzipped and Fasta formated sequence files. One sequence in file.

  getBaseSaveName 
getBaseSaveName ( self )

Assistant function that returns the default basename for output files

  showalign 
showalign ( self,  arglist )

Arguments: none prints the computed alignment to stdout


This document was automatically generated Thu Feb 19 15:16:16 2004 by HappyDoc version 3.0.a1