本文整理汇总了Python中cogent.struct.rna2d.Pairs.extend方法的典型用法代码示例。如果您正苦于以下问题：Python Pairs.extend方法的具体用法？Python Pairs.extend怎么用？Python Pairs.extend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cogent.struct.rna2d.Pairs的用法示例。
在下文中一共展示了Pairs.extend方法的2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: insert_gaps_in_pairs
# 需要导入模块: from cogent.struct.rna2d import Pairs [as 别名]
# 或者: from cogent.struct.rna2d.Pairs import extend [as 别名]
def insert_gaps_in_pairs(pairs, gap_list):
"""Adjusts numbering in pairs according to the gap list.
pairs: Pairs object
gap_list: list of integers, gap positions in a sequence
The main assumptionis that all positions in pairs correspond to
ungapped positions. If this is not true, the result will be meaningless.
"""
if not gap_list:
new = Pairs()
new.extend(pairs)
return new
ungapped = []
for idx in range(max(gap_list)+2):
if idx not in gap_list:
ungapped.append(idx)
new = Pairs()
for x,y in pairs:
if x is not None:
try:
new_x = ungapped[x]
except IndexError:
new_x = ungapped[-1] + (x-len(ungapped)+1)
else:
new_x = x
if y is not None:
try:
new_y = ungapped[y]
except IndexError:
new_y = ungapped[-1] + (y-len(ungapped)+1)
else:
new_y = y
new.append((new_x, new_y))
return new示例2: delete_gaps_from_pairs
# 需要导入模块: from cogent.struct.rna2d import Pairs [as 别名]
# 或者: from cogent.struct.rna2d.Pairs import extend [as 别名]
def delete_gaps_from_pairs(pairs, gap_list):
"""Returns Pairs object with pairs adjusted to gap_list
pairs: list of tuples or Pairs object
gap_list: list or array of gapped positions that should be removed
from the pairs object
Base pairs of which one of the partners or both of them are in
the gap list are removed. If both of them are not in the gap_list, the
numbering is adjusted according to the gap_list.
When at least one of the two pair members is in the gap_list, the
pair will be removed. The rest of the structure will be left
intact. Pairs containing None, duplicates, pseudoknots, and
conflicts will be maintained and adjusted according to the gap_list.
"""
if not gap_list:
result = Pairs()
result.extend(pairs)
return result
g = array(gap_list)
result = Pairs()
for up, down in pairs:
if up in g or down in g:
continue
else:
if up is not None:
new_up = up - g.searchsorted(up)
else:
new_up = up
if down is not None:
new_down = down - g.searchsorted(down)
else:
new_down = down
result.append((new_up, new_down))
return result