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/ mabslib / Interface.py / Interface
This class provides most of the functionality.
Most of the UI commands are related to methods of this class.
Especially align and getTFBS functions are important.
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Methods
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showMoreAlignments
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showMoreAlignments ( self, count=1 )
Gets more alignments but doesn't display them
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savematch
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savematch ( self, filename='' )
Saves the results. (possibly gziped)
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savealignGFF
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savealignGFF ( self, filename="" )
Saves the results in GFF format
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showalignSTDO
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showalignSTDO ( self )
Prints the alignment to standart out
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getSeqNames
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getSeqNames ( self )
returns the sequence names
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savealign
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savealign ( self, filename='' )
Saves the results
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addSequence
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addSequence ( self, filenames )
adds sequences from files in FASTA format
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removeMatrix
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removeMatrix ( self, index )
removes matrix given by index
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resetMatrices
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resetMatrices ( self )
resets the list of matrices
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resetSequences
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resetSequences ( self )
resets the sequences
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__init__
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__init__ ( self )
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printMatrices
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printMatrices ( self )
prints matrices to standard out
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quit
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quit ( self )
Exits the program
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savealignAnchor
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savealignAnchor ( self, filename="" )
Saves the results in Anchor format
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printMatrixWeights
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printMatrixWeights ( self )
prints matrix weights to standard out
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moreAlignments
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moreAlignments ( self, num_of_align=1 )
Fetch more alignments from previously run alignment matrix
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removeSequence
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removeSequence ( self, name )
removes sequences given by name
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align
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align (
self,
filename='.',
num_of_align=3,
Lambda=1.0,
xi=1.0,
mu=0.5,
nu=1.0,
nuc_per_rotation=10.4,
)
aligns the computed BS or some given in file
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addMatrix
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addMatrix ( self, filenames )
adds new matrices from given files
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getTFBS
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getTFBS (
self,
bound=0.1,
absCutoff=None,
)
computes the possible TFBS
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showmatch
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showmatch ( self )
Prints the results to standard out
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getTFBSAbsolute
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getTFBSAbsolute ( self, cutoff=9.0 )
computes the possible TFBS
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about
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about ( self )
Information about the program
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storeTmpGFF
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storeTmpGFF ( self )
Open temporary file and store BS data to it
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finalTmpGFF
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finalTmpGFF ( self )
Store BS data to temporary file and close it
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