[conf.PathConstrainteFile, conf.PathConstrainteFileShape],
Alignementfolder, conf.numberofsruct, conf.Temperature,
conf.Fastaextenstion, m, b)
for filz in GetListFile(path_Fasta, FileExtensionFasta):
print filz, "Treatement "
startimebig = time.time()
rna = FF.Parsefile(
os.path.join(path_Fasta, filz + '.' + FileExtensionFasta))[1]
Indexe = filz
SVMlFile = "DissimilarityMatrix" + conf.numberofsruct
listfiles = [filz + state for state in ["NMIA", "1M7", "MSA"]]
OutputSamples = 'OutputSamples' + conf.numberofsruct
MFESnbrstruct = len(
listfiles) # 1 for the case where no constraint is given
FF.MergeFiles(OutputSamples, os.path.join(OutputSamples, 'Samples.txt'),
listfiles, 1)
#endtime=time.time()
#print("Sampling done with success in %53f\t"%(endtime-startime))
#!!!!!!!!!!!!! Distance Matrix calculation !!!!!!!!!!!
#
startime = time.time()
print("Distance Matrix generation for % d Structures started " %
(int(conf.numberofsruct) * len(listfiles) + MFESnbrstruct))
Redundant = []
Newnumberofsruct = defaultdict(lambda: defaultdict())
#calculate distance
SF.DistanceStruct(os.path.join(OutputSamples, 'Samples.txt'), SVMlFile,
int(conf.numberofsruct), MFESnbrstruct, listfiles)
endtime = time.time()
if str.lower(
conf.Sampling) == "true" or not os.path.isdir(OutputSamples):
progress.StartTask("Sampling %s structures for each condition" %
(conf.SampleSize))
OutputSamples = SP.StructSampling(
[conf.PathConstraintsFile, conf.PathConstraintsFileShape],
ProbingConditions, int(conf.SampleSize), conf.Temperature,
conf.m, conf.b, conf.RNA)
progress.EndTask()
else:
progress.Print("Using existing sample")
progress.Print("Probing conditions: %s" % (ProbingConditions))
# Create a global file that contains structures sampled from the list of Probing conditions
FF.MergeFiles(OutputSamples, os.path.join(OutputSamples,
'Samples.txt'),
ProbingConditions, SP.NUM_HEADER_LINES)
# Create a distance matrix file
progress.StartTask("Computing dissimilarity matrix")
SVMlFile = "DissimilarityMatrix" + conf.SampleSize
# Calculate distance and identify redundant structures within the same condition
SF.DistanceStruct(os.path.join(OutputSamples, 'Samples.txt'), SVMlFile,
int(conf.SampleSize), ProbingConditions)
progress.EndTask()
################################# Calculate Conditional Boltzmann probabilities
# for each condition, calculate Z over all non redundant structures and return a conditional Boltzmann probability for all structures with null value for redundant ones.
progress.StartTask("Computing Boltzmann probabilities")
BoltzmannFactor = defaultdict(lambda: defaultdict())
ConditionalBoltzmannProbability = defaultdict(lambda: defaultdict())
