在从字符串中删除破折号的同时保持重叠注释

Question

假设使用以下 Python 函数从字符串中删除破折号（“空白”），同时保持该字符串上的正确注释。输入变量instring和annotations分别构成一个字符串和一个字典。

def DegapButMaintainAnno(instring, annotations):
    degapped_instring = ''
    degapped_annotations = {}
    gaps_cumulative = 0
    for range_name, index_list in annotations.items():
        gaps_within_range = 0
        for pos, char in enumerate(instring):
            if pos in index_list and char == '-':
                index_list.remove(pos)
                gaps_within_range += 1
            if pos in index_list and char != '-':
                degapped_instring += char
                index_list[index_list.index(pos)] = pos - gaps_within_range
        index_list = [i-gaps_cumulative for i in index_list]
        degapped_annotations[range_name] = index_list
        gaps_cumulative += gaps_within_range
    return (degapped_instring, degapped_annotations)

如果输入字典指定的范围没有重叠，则所述函数按预期工作：

>>> instr = "A--AT--T"
>>> annot = {"range1":[0,1,2,3,4], "range2":[5,6,7]}
>>> DegapButMaintainAnno(instr, annot)
Out: ('AATT', {'range1': [0, 1, 2], 'range2': [3]})

但是，一旦一个或多个范围重叠，代码就会失败：

>>> annot = {"range1":[0,1,2,3,4], "range2":[4,5,6,7]}
>>> DegapButMaintainAnno(instr, annot)
Out: ('AATTT', {'range1': [0, 1, 2], 'range2': [2, 3]}) # See additional 'T' in string

有人对如何纠正我的代码重叠范围有什么建议吗？

Answer 1

我觉得你可能想多了。这是我的尝试：

from copy import copy

def rewriteGene(instr, annos):
    annotations = copy(annos)
    index = instr.find('-')
    while index > -1:
        for key, ls in annotations.items():
            if index in ls:
                ls.remove(index)
            annotations[key] = [e-1 if e > index else e for e in ls]
        instr = instr[:index] + instr[index+1:]
        index = instr.find('-')
    return instr, annotations

instr = "A--AT--T"
annos = {"range1":[0,1,2,3,4], "range2":[4,5,6,7]}

print rewriteGene(instr, annos)
# ('AATT', {'range2': [2, 3], 'range1': [0, 1, 2]})

它应该很容易阅读，但如果你想澄清任何事情，请告诉我。