[Biopython] some problem parsing swissprot format

[Peter Cock]

Hi Michael,

Given updating to Biopython 1.65 fixed this, there's no real need
to work out exactly which record(s) Biopython 1.64 didn't like.

Thanks for letting us know its working now :)

Peter

On Tue, Jun 2, 2015 at 12:11 PM, Michael Thon <mike.thon at gmail.com> wrote:
> Hi Peter - I finally got back to work on this. I installed biopython 1.65
> in a virtualenv and my script works fine now. My previous version
> was 1.64. I could probably hunt down the record that breaks my
> script  if you think you need it for a test case.
> Mike
>
>
>
>> On May 29, 2015, at 12:58 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>> On Fri, May 29, 2015 at 11:24 AM, Michael Thon <mike.thon at gmail.com> wrote:
>>> I downloaded a set of proteins from uniprot in 'text' format. I am parsing the file with this:
>>>
>>> in_file = SeqIO.parse(file_h, "swiss")
>>>
>>> but I ran into this error:
>>>
>>> Traceback (most recent call last):
>>>  File "prep_blast_db.py", line 19, in <module>
>>>    for item in in_file:
>>>  File "/Library/Python/2.7/site-packages/Bio/SeqIO/__init__.py", line 586, in parse
>>>    for r in i:
>>>  File "/Library/Python/2.7/site-packages/Bio/SeqIO/SwissIO.py", line 81, in SwissIterator
>>>    for swiss_record in swiss_records:
>>>  File "/Library/Python/2.7/site-packages/Bio/SwissProt/__init__.py", line 117, in parse
>>>    record = _read(handle)
>>>  File "/Library/Python/2.7/site-packages/Bio/SwissProt/__init__.py", line 184, in _read
>>>    _read_rn(reference, value)
>>>  File "/Library/Python/2.7/site-packages/Bio/SwissProt/__init__.py", line 409, in _read_rn
>>>    assert rn[0] == '[' and rn[-1] == ']', "Missing brackets %s" % rn
>>> AssertionError: Missing brackets [1] {ECO:0000305, ECO:0000312|EMBL:BAC84995.1}
>>>
>>> Maybe swissprot format has changed?
>>
>> Hi Michael,
>>
>> Yes, the format did change - but it sounds like something which should
>> already be fixed in Biopython 1.65,
>>
>> https://github.com/biopython/biopython/issues/513
>> https://github.com/biopython/biopython/issues/369
>>
>> Which version of Biopython are you using, and can you update it?
>>
>> Which record from UniProt causes this problem (so we can test it)?
>>
>> Thanks,
>>
>> Peter
>