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- bg_from_sequence(seq, ps)
- count_log_odds(matrix, bg, ps)
- Calculates a log-odds matrix from a position frequency matrix
- flatbg(size=4)
- Creates a flat background distribution table
- load_matrix(filename)
- Loads a matrix from a file given.
Returns matrix as an array of arrays of numbers.
- max_score(matrix)
- Calculates a maximum score of matrix
- reverse_complement(matrix)
- Creates a reverse complement of PWM
- search(sequence, matrices, thresholds, bg=None, algorithm='lf', q=7, absolute_threshold=False, both_strands=False, combine=True)
- Finds position weight matrix matches in dna sequence.
Returns :
An array of references to result arrays. There are one result
array corresponding to each matrix.
Each result array is a list of tuples of position and score
like: [(pos1, score1), (pos2, score2) ...]
Parameters:
Obligatory:
sequence python string object
matrices
One matrix is represented as a typical python multidimensional
array. An array of matrices is expected here.
thresholds
This can be a number, if you want to use the same threshold for
all matrices, but you can give multiple thresholds as well.
Multiple thresholds are given as an array of numbers.
Optional
bg
Background distribution - an array of four doubles. By default
the background is calculated from sequence.
algorithm
You can switch search algorithm (Doesn't affect on results)
"naive" naive algorithm
"pla" permutated lookahead algorithm
"supera" super alphabet algorithm.
- Good for long matrices (> 20)
"lf" lookahead filtration algorithm.
- Default algorithm in most cases.
- Sequence can be searched with multiple matrices
simultaneously.
- You should use this when you have large amount of matrices.
q You can optionally give a parameter for algorithm (Doesn't
change results) You can try different values to improve
performance.
absolute_threshold
True if thresholds is given as an absolute value instead of p.
both_strands
You can search for both dna strands.
- threshold_from_p(matrix, bg, p)
- Calculates an absolute threshold from a probability value
- total_matches(matchArray)
- Calculates a total number of matches.
- transpose(matrix)
- Creates a transpose of matrix array
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