diff options
Diffstat (limited to 'pangraph/sequence.py')
| -rw-r--r-- | pangraph/sequence.py | 78 |
1 files changed, 66 insertions, 12 deletions
diff --git a/pangraph/sequence.py b/pangraph/sequence.py index b2b5ce7..db2b3e6 100644 --- a/pangraph/sequence.py +++ b/pangraph/sequence.py @@ -88,12 +88,6 @@ class Path(object): return seq - def position_of(self, blk): - for i, n in enumerate(self.nodes): - if n.blk == blk: - return i, n.num - raise ValueError("block not found in path") - def rm_nil_blks(self): good, popped = [], set() for i, n in enumerate(self.nodes): @@ -121,6 +115,8 @@ class Path(object): try: i, j = ids.index(start[0]), ids.index(stop[0]) + if N > 0: + breakpoint("HIT") if self.nodes[i].strand == start[1]: beg, end, s = i, j, Strand.Plus else: @@ -153,17 +149,75 @@ class Path(object): self.nodes = new self.position = np.cumsum([0] + [n.length(self.name) for n in self.nodes]) + def position_of(self, blk, num): + index = { n.num:i for i, n in enumerate(self.nodes) if n.blk == blk } + if not num in index: + return None + return (self.position[index[num]], self.position[index[num]+1]) + + def orientation_of(self, blk, num): + orientation = { n.num:n.strand for i, n in enumerate(self.nodes) if n.blk == blk } + if not num in orientation: + return None + return orientation[num] + + # TODO: pull out common functionality into a helper function + # TODO: merge with other sequence function + def sequence_range(self, start=None, stop=None): + beg = start or 0 + end = stop or self.position[-1] + l, r = "", "" + if beg < 0: + if len(self.nodes) > 1: + l = self.sequence_range(self.position[-1]+beg,self.position[-1]) + beg = 0 + if end > self.position[-1]: + if len(self.nodes) > 1: + r = self.sequence_range(0,end-self.position[-1]) + end = self.position[-1] + if beg > end: + beg, end = end, beg + + i = np.searchsorted(self.position, beg, side='right') - 1 + j = np.searchsorted(self.position, end, side='left') + m = "" + if i < j: + if j >= len(self.position): + breakpoint("what?") + if i == j - 1: + m = self.nodes[i].blk.extract(self.name, self.nodes[i].num)[(beg-self.position[i]):(end-self.position[i])] + else: + m = self.nodes[i].blk.extract(self.name, self.nodes[i].num)[(beg-self.position[i]):] + for n in self.nodes[i+1:j-1]: + m += n.blk.extract(self.name, n.num) + n = self.nodes[j-1] + b = n.blk.extract(self.name, n.num) + m += b[0:(end-self.position[j-1])] + return l + m + r + def __getitem__(self, index): if isinstance(index, slice): beg = index.start or 0 end = index.stop or self.position[-1] - - i = np.searchsorted(self.position, beg, side='right') - j = np.searchsorted(self.position, end, side='right') + 1 - assert i < j, "sorted" - return [n.blk for n in self.nodes[i:j]] + l, r = [], [] + if beg < 0: + if len(self.nodes) > 1: + l = self[(self.position[-1]+beg):self.position[-1]] + beg = 0 + if end > self.position[-1]: + if len(self.nodes) > 1: + r = self[0:(end-self.position[-1])] + end = self.position[-1] + if beg > end: + beg, end = end, beg + + i = np.searchsorted(self.position, beg, side='right') - 1 + j = np.searchsorted(self.position, end, side='left') + if i > j: + breakpoint(f"not sorted, {beg}-{end}") + return l + [n.blk for n in self.nodes[i:j]] + r elif isinstance(index, int): - i = np.searchsorted(self.position, index, side='left') + i = np.searchsorted(self.position, index, side='right') - 1 return self.nodes[i].blk else: raise ValueError(f"type '{type(index)}' not supported as index") |