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BIOtoStandoff.py
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BIOtoStandoff.py
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#!/usr/bin/env python
# Script to convert a column-based BIO-formatted entity-tagged file
# into standoff with reference to the original text.
import re
import sys
class taggedEntity:
def __init__(self, startOff, endOff, eType, idNum, fullText):
self.startOff = startOff
self.endOff = endOff
self.eType = eType
self.idNum = idNum
self.fullText = fullText
self.eText = fullText[startOff:endOff]
def __str__(self):
return "T%d\t%s %d %d\t%s" % (self.idNum, self.eType, self.startOff,
self.endOff, self.eText)
def check(self):
# sanity checks: the string should not contain newlines and
# should be minimal wrt surrounding whitespace
assert "\n" not in self.eText, \
"ERROR: newline in entity: '%s'" % self.eText
assert self.eText == self.eText.strip(), \
"ERROR: entity contains extra whitespace: '%s'" % self.eText
def BIO_to_standoff(BIOtext, reftext, tokenidx=2, tagidx=-1):
BIOlines = BIOtext.split('\n')
return BIO_lines_to_standoff(BIOlines, reftext, tokenidx, tagidx)
next_free_id_idx = 1
def BIO_lines_to_standoff(BIOlines, reftext, tokenidx=2, tagidx=-1):
global next_free_id_idx
taggedTokens = []
ri, bi = 0, 0
while(ri < len(reftext)):
if bi >= len(BIOlines):
print("Warning: received BIO didn't cover given text", file=sys.stderr)
break
BIOline = BIOlines[bi]
if re.match(r'^\s*$', BIOline):
# the BIO has an empty line (sentence split); skip
bi += 1
else:
# assume tagged token in BIO. Parse and verify
fields = BIOline.split('\t')
try:
tokentext = fields[tokenidx]
except BaseException:
print("Error: failed to get token text " \
"(field %d) on line: %s" % (tokenidx, BIOline), file=sys.stderr)
raise
try:
tag = fields[tagidx]
except BaseException:
print("Error: failed to get token text " \
"(field %d) on line: %s" % (tagidx, BIOline), file=sys.stderr)
raise
m = re.match(r'^([BIO])((?:-[A-Za-z0-9_-]+)?)$', tag)
assert m, "ERROR: failed to parse tag '%s'" % tag
ttag, ttype = m.groups()
# strip off starting "-" from tagged type
if len(ttype) > 0 and ttype[0] == "-":
ttype = ttype[1:]
# sanity check
assert ((ttype == "" and ttag == "O") or
(ttype != "" and ttag in ("B", "I"))), \
"Error: tag/type mismatch %s" % tag
# go to the next token on reference; skip whitespace
while ri < len(reftext) and reftext[ri].isspace():
ri += 1
# verify that the text matches the original
assert reftext[ri:ri + len(tokentext)] == tokentext, \
"ERROR: text mismatch: reference '%s' tagged '%s'" % \
(reftext[ri:ri + len(tokentext)].encode("UTF-8"),
tokentext.encode("UTF-8"))
# store tagged token as (begin, end, tag, tagtype) tuple.
taggedTokens.append((ri, ri + len(tokentext), ttag, ttype))
# skip the processed token
ri += len(tokentext)
bi += 1
# ... and skip whitespace on reference
while ri < len(reftext) and reftext[ri].isspace():
ri += 1
# if the remaining part either the reference or the tagged
# contains nonspace characters, something's wrong
if (len([c for c in reftext[ri:] if not c.isspace()]) != 0 or
len([c for c in BIOlines[bi:] if not re.match(r'^\s*$', c)]) != 0):
assert False, "ERROR: failed alignment: '%s' remains in reference, " \
"'%s' in tagged" % (reftext[ri:], BIOlines[bi:])
standoff_entities = []
# cleanup for tagger errors where an entity begins with a
# "I" tag instead of a "B" tag
revisedTagged = []
prevTag = None
for startoff, endoff, ttag, ttype in taggedTokens:
if prevTag == "O" and ttag == "I":
print("Note: rewriting \"I\" -> \"B\" after \"O\"", file=sys.stderr)
ttag = "B"
revisedTagged.append((startoff, endoff, ttag, ttype))
prevTag = ttag
taggedTokens = revisedTagged
# cleanup for tagger errors where an entity switches type
# without a "B" tag at the boundary
revisedTagged = []
prevTag, prevType = None, None
for startoff, endoff, ttag, ttype in taggedTokens:
if prevTag in ("B", "I") and ttag == "I" and prevType != ttype:
print("Note: rewriting \"I\" -> \"B\" at type switch", file=sys.stderr)
ttag = "B"
revisedTagged.append((startoff, endoff, ttag, ttype))
prevTag, prevType = ttag, ttype
taggedTokens = revisedTagged
prevTag, prevEnd = "O", 0
currType, currStart = None, None
for startoff, endoff, ttag, ttype in taggedTokens:
if prevTag != "O" and ttag != "I":
# previous entity does not continue into this tag; output
assert currType is not None and currStart is not None, \
"ERROR in %s" % fn
standoff_entities.append(taggedEntity(currStart, prevEnd, currType,
next_free_id_idx, reftext))
next_free_id_idx += 1
# reset current entity
currType, currStart = None, None
elif prevTag != "O":
# previous entity continues ; just check sanity
assert ttag == "I", "ERROR in %s" % fn
assert currType == ttype, "ERROR: entity of type '%s' continues " \
"as type '%s'" % (currType, ttype)
if ttag == "B":
# new entity starts
currType, currStart = ttype, startoff
prevTag, prevEnd = ttag, endoff
# if there's an open entity after all tokens have been processed,
# we need to output it separately
if prevTag != "O":
standoff_entities.append(taggedEntity(currStart, prevEnd, currType,
next_free_id_idx, reftext))
next_free_id_idx += 1
for e in standoff_entities:
e.check()
return standoff_entities
RANGE_RE = re.compile(r'^(-?\d+)-(-?\d+)$')
def parse_indices(idxstr):
# parse strings of forms like "4,5" and "6,8-11", return list of
# indices.
indices = []
for i in idxstr.split(','):
if not RANGE_RE.match(i):
indices.append(int(i))
else:
start, end = RANGE_RE.match(i).groups()
for j in range(int(start), int(end)):
indices.append(j)
return indices
def main(argv):
if len(argv) < 3 or len(argv) > 5:
print("Usage:", argv[0], "TEXTFILE BIOFILE [TOKENIDX [BIOIDX]]", file=sys.stderr)
return 1
textfn, biofn = argv[1], argv[2]
tokenIdx = None
if len(argv) >= 4:
tokenIdx = int(argv[3])
bioIdx = None
if len(argv) >= 5:
bioIdx = argv[4]
with open(textfn, 'rU') as textf:
text = textf.read()
with open(biofn, 'rU') as biof:
bio = biof.read()
if tokenIdx is None:
so = BIO_to_standoff(bio, text)
elif bioIdx is None:
so = BIO_to_standoff(bio, text, tokenIdx)
else:
try:
indices = parse_indices(bioIdx)
except BaseException:
print('Error: failed to parse indices "%s"' % bioIdx, file=sys.stderr)
return 1
so = []
for i in indices:
so.extend(BIO_to_standoff(bio, text, tokenIdx, i))
for s in so:
print(s)
return 0
if __name__ == "__main__":
sys.exit(main(sys.argv))