def run(self):
pos = RegionSelection()
seq = RegionSelection()
_pos = iter(self.target.selection.positions.regions)
_seq = iter(self.target.selection.sequences.regions)
_areas = (a.positions for a in self.target.selection.areas.areas)
for pos_region in sorted(chain(_pos, _areas), key=lambda r: r.start):
pos.incorporate(pos_region)
for seq_region in sorted(chain(_seq, _areas), key=lambda r: r.start):
seq.incorporate(seq_region)
if not pos.regions:
pos.add_region(0, len(self.target))
if not seq.regions:
seq.add_region(0, len(self.target.sequences))
sequences = [list() for _ in range(sum(r.length for r in seq.regions))]
ids = [None] * len(sequences)
descriptions = [None] * len(sequences)
new_index = -1
for seq_region in seq.regions:
for i, sequence in enumerate(self.target.sequences[seq_region.start:seq_region.start + seq_region.length]):
new_index += 1
sequences[new_index] = ''.join(sequence[r.start:r.start+r.length] for r in pos.regions)
ids[new_index] = self.target.ids[seq_region.start + i]
descriptions[new_index] = self.target.ids[seq_region.start + i]
self.target.selection.positions.clear()
self.target.selection.sequences.clear()
self.target.selection.areas.clear()
path = self.target.path.strip('*') + '*'
self.target.set_msa(sequences, path, ids, descriptions)
def run(self):
sel = RegionSelection()
positions = iter(self.target.selection.positions.regions)
areas = (a.positions for a in self.target.selection.areas.areas)
for region in sorted(chain(positions, areas), key=lambda r: r.start):
sel.incorporate(region)
sel.invert(len(self.target))
sequences = []
for sequence in self.target.sequences:
sequences.append(''.join(sequence[r.start:r.start+r.length] for r in sel.regions))
self.target.selection.positions.clear()
self.target.selection.areas.clear()
path = self.target.path.strip('*') + '*'
self.target.set_msa(sequences, path, self.target.ids, self.target.descriptions)
