def translate(word):
return [{"A":0, "T":1, "G":2, "C":3}[i] for i in word]
def translateRaw(array):
return "".join([{0:"A", 1:"T", 2:"G", 3:"C"}[i] for i in array])
scoreFolder = sys.argv[1]
upstreamList = sys.argv[2]
fullUpstreamList = sys.argv[3]
if not os.path.exists("temp"):
os.mkdir("temp")
current = PatternFinder(6, "temp")
current.loadSequences(upstreamList)
full = PatternFinder(6, scoreFolder)
full.loadSequences(fullUpstreamList)
temp = PatternFinder(6, scoreFolder)
def makeTextShuffleControl(filename, minLen=10000):
cdata = np.array([translate(i.replace("\n", "").replace("\r", "")) for i in open(filename).readlines() if len(i) > 10]).T
controls = []
repeat = 1 + minLen / len(cdata[0])
for _ in xrange(repeat):
if verbose:
print "Eigenvalues are:", latent
return (np.transpose(coeff[:, ::-1]), latent[::-1])
def translate(word):
return [{"A":0, "T":1, "G":2, "C":3}[i] for i in word]
def translateRaw(array):
return "".join([{0:"A", 1:"T", 2:"G", 3:"C"}[i] for i in array])
a = PatternFinder(6, scoreFolder)
a.loadSequences(sequenceFile)
allSeqs = a.rawSequences
data = pd.read_csv(os.path.join(scoreFolder, "sortedBy/Best10000_sortBy_ScoreNew_8.csv"))
lef = data["Pos l"].values
rig = data["Pos r"].values
mask = (abs(rig - POSITION_RIGHT) < 4) * (abs(lef - POSITION_LEFT) < 4)
data = data[mask]
patLeftBest = data["Patt l"].values[0]
patRightBest = data["Patt r"].values[0]
data = data[:300]
assert len(data) > 90 # check that we have at least 90 unique patterns
allPats = []
BEST_SINGLE is the number of best n-mers to use for each side of the pattern.
Then all pairwise combinations of BEST_SINGLE x BEST_SINGLE 6-mers will be evaluated at
every pari of positions in the upstream
MAX_SCORE is the maximum score (offset + extension + mismatches) for the whole pattern
MAX_SCORE_SINGLE is the maximum score for scoring separate n-mers (used for selection of BEST_SINGLE only)
MAX_SUBS and MAX_SHIFT are maximum number of subs and maximum offset of a pattern
"""
a = PatternFinder(6, sys.argv[2])
# create a patternFinder object bound to folder provided as a second command line argument
a.loadSequences(sys.argv[1])
# if third argument is provided, we interpret it as a set of locations where to evaluate pattern
if len(sys.argv) >= 4:
locations = [map(int, j.split("-")) for j in sys.argv[3].split(",")]
print locations
# If not provided, the program will automatically select it
else:
locations = None
a.scorePatternsThroughBest(
bestNum=BEST_SINGLE,
maxScore=MAX_SCORE,
def translate(word):
return [{"A":0, "T":1, "G":2, "C":3}[i] for i in word]
def translateRaw(array):
return "".join([{0:"A", 1:"T", 2:"G", 3:"C"}[i] for i in array])
scoreFolder = sys.argv[1]
upstreamList = sys.argv[2]
fullUpstreamList = sys.argv[3]
if not os.path.exists("temp"):
os.mkdir("temp")
current = PatternFinder(6, "temp")
current.loadSequences(upstreamList)
full = PatternFinder(6, scoreFolder)
full.loadSequences(fullUpstreamList)
temp = PatternFinder(6, scoreFolder)
def makeTextShuffleControl(filename, minLen=10000):
cdata = np.array([translate(i.replace("\n", "").replace("\r", "")) for i in open(filename).readlines() if len(i) > 10]).T
controls = []
repeat = 1 + minLen / len(cdata[0])
for _ in xrange(repeat):