[Biopython-dev] SwissProt fails to parse the current uniprot_sprot data file?

[Jinghua (Frank) Feng]

Hello,

It looks like SwissProt can parse old version uniprot_sprot data file, 
but fails with the current version data file. Below is how to replicate 
the error (Biopython version is '1.64').

Regards,

Jinghua
----------------------

First download the current uniprot_sprot data file (~72 MB in size) at 
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_human.dat.gz 


Then in IPython, using SwissProt to parse the downloaded data file:

In [1]: from Bio import SwissProt

In [2]: import gzip

In [3]: inhandle = gzip.open('./uniprot_sprot_human.dat.gz')

In [4]: reader = SwissProt.parse(inhandle)

In [5]: for r in reader:
    ...:     pass
    ...:
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-5-c04351d992d2> in <module>()
----> 1 for r in reader:
       2     pass
       3

/usr/local/lib/python2.7/dist-packages/Bio/SwissProt/__init__.pyc in 
parse(handle)
     115 def parse(handle):
     116     while True:
--> 117         record = _read(handle)
     118         if not record:
     119             return

/usr/local/lib/python2.7/dist-packages/Bio/SwissProt/__init__.pyc in 
_read(handle)
     182         elif key == 'RN':
     183             reference = Reference()
--> 184             _read_rn(reference, value)
     185             record.references.append(reference)
     186         elif key == 'RP':

/usr/local/lib/python2.7/dist-packages/Bio/SwissProt/__init__.pyc in 
_read_rn(reference, rn)
     407
     408 def _read_rn(reference, rn):
--> 409     assert rn[0] == '[' and rn[-1] == ']', "Missing brackets %s" 
% rn
     410     reference.number = int(rn[1:-1])
     411

AssertionError: Missing brackets [1] {ECO:0000305, 
ECO:0000312|EMBL:AAK11482.1}



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