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/ mabslib / Commandline.py / Commandline
This is a command line based user interface.
The mabs commands and most of the default values are set here.
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Methods
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printMatrices
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printMatrices ( self, arglist )
Arguments: none
prints the matrices
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isCommand
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isCommand ( self, command )
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savematch
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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
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run
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run ( self )
waits for std input and executes these commands
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help
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help ( self, arglist )
Arguments: none
prints this help
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saveMarkovBackground
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saveMarkovBackground ( self, arglist=None )
Arguments: filename
Name of the file where to store the background model.
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savealign
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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
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addSequence
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addSequence ( self, arglist )
Arguments: filelist
reads sequences from files
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setMarkovBG
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setMarkovBG ( self, arglist=None )
Arguments: bgSampleSequence [order]
Background sample sequence and order of the model or saved background file.
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getTFBSabsolute
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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
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setPseudoCnt
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setPseudoCnt ( self, arglist=( "1.0" ) )
Arguments: [pseudocount]
Set the amount of pseudocounts on matricies. Default 1.0
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setBGFreq
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setBGFreq ( self, arglist=None )
Arguments: A C G T
Background nucleotide frequencies. Removes markov background.
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removeMatrix
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removeMatrix ( self, arglist )
Arguments: Matrixnumber
removes a matrix
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resetMatrices
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resetMatrices ( self, arglist )
Arguments: none
removes all matrices
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printSeqNames
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printSeqNames ( self, arglist )
Arguments: none
prints the names of the sequences
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__init__
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__init__ ( self )
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savealignGFF
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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
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reset
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reset ( self, arglist )
Arguments: none
removes all matrices and sequences
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quit
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quit ( self, arglist )
Arguments: none
to exit the program
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execute
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execute ( self, command )
executes the given command (like run does)
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printMatrixWeights
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printMatrixWeights ( self, arglist )
Arguments: none
prints the matrix weights (with background)
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savealignAnchor
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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
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removeSequence
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removeSequence ( self, arglist )
Arguments: Sequencename
removes a sequence
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align
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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.
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addMatrix
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addMatrix ( self, arglist )
Arguments: filelist
reads matrices from files
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getTFBS
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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
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resetSequences
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resetSequences ( self, arglist )
Arguments: none
removes all sequences
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showmatch
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showmatch ( self, arglist )
Arguments: none
prints the computed scores to stdout
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moreAlignment
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moreAlignment ( self, arglist=( 1, ) )
Arguments: [number of alignments]
prints more alignments from previously run alignment matrix
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about
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about ( self, arglist )
Arguments: none
Prints Information about the program
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addSingleSequence
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addSingleSequence ( self, arglist )
Arguments: filelist
Gzipped and Fasta formated sequence files. One sequence in file.
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getBaseSaveName
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getBaseSaveName ( self )
Assistant function that returns the default basename for output files
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showalign
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showalign ( self, arglist )
Arguments: none
prints the computed alignment to stdout
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