本文整理汇总了Python中RNA.doubleP_getitem方法的典型用法代码示例。如果您正苦于以下问题：Python RNA.doubleP_getitem方法的具体用法？Python RNA.doubleP_getitem怎么用？Python RNA.doubleP_getitem使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类RNA的用法示例。
在下文中一共展示了RNA.doubleP_getitem方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: main
# 需要导入模块: import RNA [as 别名]
# 或者: from RNA import doubleP_getitem [as 别名]
def main():
usage = """
python scripts/dotplus.py sequence
Create a file for displaying as a dotplot using the provided sequence.
If the provided sequence is '-', then read the sequence from stdin.
"""
num_args= 1
parser = OptionParser(usage=usage)
parser.add_option('-p', '--probability', dest='probability', default=0.01, help="The probability cutoff for displaying base pair points", type='float')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
if args[0] == '-':
seq = sys.stdin.read()
else:
seq = args[0].strip()
# pf_fold returns the MFE as well as the partition function energy
mfe, pfe = RNA.pf_fold(seq)
prob_matrix = RNA.export_bppm()
bp_to_seq = {}
# get all of the suboptimal structures
subopts = RNA.zukersubopt(seq)
for i in range(0, subopts.size()):
s = subopts.get(i)
pt = fus.dotbracket_to_pairtable(s.structure)
# go through each base pair and store the sequence
# it came from so that it can be output later
for j in range(1, pt[0]+1):
bp = tuple(sorted([j, pt[j]]))
if bp in bp_to_seq:
continue
bp_to_seq[bp] = (s.structure, s.energy)
#print s.structure, s.energy
bps = []
structs = []
counter = 0
struct_dict = {}
base_probs = col.defaultdict(float)
print >>sys.stderr, "probability:", options.probability
for i,j in it.combinations(range(1, len(seq)+1), 2):
prob = RNA.doubleP_getitem(prob_matrix,
RNA.intP_getitem(RNA.cvar.iindx, i) - j)
base_probs[i] += prob
base_probs[j] += prob
if prob > options.probability:
struct, energy = bp_to_seq[(i,j)]
pp = math.exp((pfe - (energy / 100.)) / .616310776)
if struct not in struct_dict:
struct_dict[struct] = (struct, pp, counter)
index = counter
counter += 1
else:
index = struct_dict[struct][2]
print >>sys.stderr, "ix:", index, "struct:", struct, "pp:", pp
bps += [{"i": i, "j": j, "p": "{:.3f}".format(math.sqrt(prob)), "ix": index}]
structs = struct_dict.values()
structs.sort(key=lambda x: -x[1])
base_probs = dict([(i, "{:.3f}".format(j)) for (i,j) in base_probs.items()])
structs = [{"struct": st[0], "sprob": st[1], "ix": st[2]} for st in structs]
print json.dumps({"seq": seq, "structs": structs, "bps": bps, "baseProbs": base_probs.items()}, indent=2)