import QPalmaDP
import qpalma
-from qpalma.SIQP_CPX import SIQPSolver
+#from qpalma.SIQP_CPX import SIQPSolver
#from qpalma.SIQP_CVXOPT import SIQPSolver
+import array
from qpalma.DataProc import *
from qpalma.computeSpliceWeights import *
# Initialize solver
self.plog('Initializing problem...\n')
- try:
- solver = SIQPSolver(run['numFeatures'],numExamples,run['C'],self.logfh,run)
- except:
- self.plog('Got no license. Telling queue to reschedule job...\n')
- sys.exit(99)
+ #try:
+ # solver = SIQPSolver(run['numFeatures'],numExamples,run['C'],self.logfh,run)
+ #except:
+ # self.plog('Got no license. Telling queue to reschedule job...\n')
+ # sys.exit(99)
#solver.enforceMonotonicity(lengthSP,lengthSP+donSP)
#solver.enforceMonotonicity(lengthSP+donSP,lengthSP+donSP+accSP)
true_map[0] = 1
pathNr = 0
- _newSpliceAlign = newSpliceAlign.flatten().tolist()[0]
- _newEstAlign = newEstAlign.flatten().tolist()[0]
+ _newSpliceAlign = array.array('B',newSpliceAlign.flatten().tolist()[0])
+ _newEstAlign = array.array('B',newEstAlign.flatten().tolist()[0])
alignment = get_alignment(_newSpliceAlign,_newEstAlign, dna_array, est_array) #(qStart, qEnd, tStart, tEnd, num_exons, qExonSizes, qStarts, qEnds, tExonSizes, tStarts, tEnds)
+
+ dna_array = array.array('c',dna_array)
+ est_array = array.array('c',est_array)
+
#line1,line2,line3 = pprint_alignment(_newSpliceAlign,_newEstAlign, dna_array, est_array)
#self.plog(line1+'\n')
#self.plog(line2+'\n')
newExons = self.calculatePredictedExons(newSpliceAlign)
current_prediction = {'predExons':newExons, 'dna':dna, 'est':est, 'DPScores':newDPScores,\
- 'alignment':alignment}
+ 'alignment':alignment,\
+ 'spliceAlign':_newSpliceAlign,'estAlign':_newEstAlign,\
+ 'dna_array':dna_array, 'est_array':est_array }
return current_prediction