[Biopython] some problem parsing swissprot format

[Peter Cock]

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