Steven Bethard wrote:
> I have some plain text data and some SGML markup for that text that I
> need to align. (The SGML doesn't maintain the original whitespace, so I
> have to do some alignment; I can't just calculate the indices directly.)
[snip]
> Note that the SGML inserts spaces not only within the SGML elements, but
> also around punctuation.
[snip]
> I need to determine the indices in the original text that each SGML
> element corresponds to.
Ok, below is a working version that doesn't use regular expressions.
It's far from concise, but at least it doesn't fail like re does when I
have more than 100 words. =)
>>> import elementtree.ElementTree as etree
>>> def align(text, sgml):
... # convert SGML tree to words, and assemble a list of the
... # start word index and end word index for each SGML element
... sgml = sgml.replace('&', '&')
... tree = etree.fromstring('<xml>%s</xml>' % sgml)
... words = []
... if tree.text is not None:
... words.extend(tree.text.split())
... word_spans = []
... for elem in tree:
... elem_words = elem.text.split()
... start = len(words)
... end = start + len(elem_words)
... word_spans.append((start, end, elem.tag))
... words.extend(elem_words)
... if elem.tail is not None:
... words.extend(elem.tail.split())
... # determine the start character index and end character index
... # for each word from the SGML
... char_spans = []
... start = 0
... for word in words:
... while text[start:start + 1].isspace():
... start += 1
... end = start + len(word)
... assert text[start:end] == word, (text[start:end], word)
... char_spans.append((start, end))
... start = end
... # convert the word indices for each SGML element to
... # character indices
... for word_start, word_end, label in word_spans:
... start, _ = char_spans[word_start]
... _, end = char_spans[word_end - 1]
... yield label, start, end
...
>>> text = '''TNF binding induces release of AIP1 (DAB2IP) from TNFR1,
resulting in cytoplasmic translocation and concomitant formation of an
intracellular signaling complex comprised of TRADD, RIP1, TRAF2, and
AIPl.'''
>>> sgml = '''<PROTEIN> TNF </PROTEIN> binding induces release of
<PROTEIN> AIP1 </PROTEIN> ( <PROTEIN> DAB2IP </PROTEIN> ) from <PROTEIN>
TNFR1 </PROTEIN> , resulting in cytoplasmic translocation and
concomitant formation of an <PROTEIN> intracellular signaling complex
</PROTEIN> comprised of <PROTEIN> TRADD </PROTEIN> , <PROTEIN> RIP1
</PROTEIN> , <PROTEIN> TRAF2 </PROTEIN> , and AIPl .
... '''
>>> list(align(text, sgml))
[('PROTEIN', 0, 3), ('PROTEIN', 31, 35), ('PROTEIN', 37, 43),
('PROTEIN', 50, 55), ('PROTEIN', 128, 159), ('PROTEIN', 173, 178),
('PROTEIN', 180, 184), ('PROTEIN', 186, 191)]
STeVe
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