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
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
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
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 equal(g, up).any() or equal(g, down).any():
continue
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
