[Biopython] some problem parsing swissprot format
Michael Thon
mike.thon at gmail.com
Fri May 29 10:24:39 UTC 2015
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?
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