To reproduce the error:
$ wget http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.zip
$ python
Python 2.7.4 (default, Sep 26 2013, 03:20:26)
[GCC 4.7.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from zipfile import ZipFile
>>>
>>> with ZipFile("dbNSFP2.0.zip", "r") as zf:
... with zf.open("dbNSFP2.0_variant.chr20", "U") as f:
... count = 0
... for line in f:
... count += 1
...
>>> print count
964352
$ unzip -p dbNSFP2.0.zip dbNSFP2.0_variant.chr20 | wc -l
2161277
may it be related to issue 6759 ?