def rnaf_exec(r,w,args):
sq=""
if (args.filename != None):
if args.filename.endswith('.fasta'):
sq = fasta_iter(args.filename).next()[1]
else:
with open(args.filename, "r") as inFile:
sq = inFile.read()
else:
print("Enter a sequence; press CTRL+D twice when done.")
sq = r.read()
sq = sq.lower()
sq = sq.replace(" ", "")
sq = sq.replace("\n", "")
sq =sq.replace("t","u")
possibleHelices = rnaf_evalSequence(sq, args.minloopsize, args.maxloopsize, args.minlength, args.maxlength)
rnaf_findEnergetics(possibleHelices, sq)
# rnaf_pDict(possibleHelices, w)
if args.graph:
rnaf_writeToFileWebGraph(possibleHelices)
if args.helicesout:
rnaf_writeToFileGauss(possibleHelices)
return possibleHelices
else:
return possibleHelices
import json
'''
All possible helices predictions, mainly written by previous class.
'''
parser = argparse.ArgumentParser(description="Give an input .fasta or a user defined sequence and this will predict and filter primary helices. May provide configuration parameter file and reference PieSie for validation.")
parser.add_argument("filename", nargs='?', help="File containing input sequence", default=None)
parser.add_argument("-p", "--params", help="File containing json filtering parameters", default=None)
parser.add_argument("-r", "--piesie", help="File containing correct structure annotations (piesie file)", default=None)
parser.add_argument("-o", "--outpred", help="Include this flag to output filtered helices data frame", default=None)
args = parser.parse_args()
if (args.filename != None):
if args.filename.endswith('.fasta'):
sq = annotate.fasta_iter(args.filename).next()[1]
outfile = args.filename.replace('.fasta', '.helices')
else:
sq = raw_input("Enter a sequence and press enter: ")
sq = sq.lower()
sq = sq.replace(" ", "")
sq =sq.replace("t","u")
if args.params != None:
params_file = open(args.params)
params = json.loads(params_file.read())
else:
print 'You Can Input Params -p <file>'
print "Just using default params for this run"
params = {
"minloopsize": 3,
