def bayesfold(seqsin, temperature=37, params=None):
'''Takes in sequences in LoadSeqs readable format and returns
most likely structure from bayesfold.'''
try:
if params == None:
params = {}
aln = align_unaligned_seqs(seqsin, RNA, params=params)
bayesinput = BayesInputWrapper(aln.getSeqNames(),
map(str, aln.iterSeqs()), str(temperature))
bayescalc = BayesCalculation(bayesinput)
bayescalc.run()
struct = str(bayescalc.Alignment.Structures).split()[1]
del bayescalc
del bayesinput
return aln, struct
except Exception, e:
print "BAYESFOLD ERROR: ", e
def bayesfold(seqsin, temperature=37, params=None, align=True):
'''Takes in sequences in LoadSeqs readable format and returns
most likely structure from bayesfold.'''
try:
if params is None:
params = {}
if not align:
aln = LoadSeqs(data=seqsin, moltype=RNA, aligned=True)
else:
aln = align_unaligned_seqs(seqsin, RNA, params=params)
bayesinput = BayesInputWrapper(aln.getSeqNames(),
map(str, aln.iterSeqs()),
str(temperature))
bayescalc = BayesCalculation(bayesinput)
bayescalc.run()
struct = str(bayescalc.Alignment.Structures).split()[1]
del bayescalc
del bayesinput
return aln, struct
except Exception, e:
print "BAYESFOLD ERROR: ", format_exc(e)
raise RuntimeError("BAYESFOLD ERROR: ", format_exc(e))
from cogent.parse.fasta import MinimalFastaParser
from sys import argv
from cogent import LoadSeqs, RNA
class BayesWrapper:
def __init__(self,name,labels,seqs):
self.name = name
self.temperature = '37'
self.primer3 = ''
self.primer5 = ''
self.labels = labels
self.sequences = seqs
self.mappings = []
self.id = '12345'
if __name__ == "__main__":
aln = LoadSeqs(argv[1], moltype=RNA)
headers = aln.getSeqNames()
seqs = map(str, aln.iterSeqs())
print headers
print seqs
test = BayesWrapper('test', headers, seqs)
temperature = 37
bayescalc = BayesCalculation(test)
bayescalc.run()
print str(bayescalc.Alignment.Structures).split()[1]
#sequences = RNAAlignment(sequences=seqs)
#structures = sequences.fold(temperature, 2, 100)
#alignment = RNAStructureAlignment(sequences,structures,temperature).Structures
#print str(alignment).split("\n")[0]
