[Biopython-dev] Consumer of "KW" in embl format
Peter Cock
p.j.a.cock at googlemail.com
Tue Mar 12 15:13:23 UTC 2013
On Tue, Mar 12, 2013 at 2:40 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Tue, Mar 12, 2013 at 11:35 AM, Xabier Bello <xbello at gmail.com> wrote:
>> Lets try it:
>>
>> Line 997:
>> def _write_keywords(self, record):
>> #Put the keywords right after DE line.
>> self._write_multi_line("KW", "%s." % "; ".join(
>> record.annotations["keywords"]))
>> self.handle.write("XX\n")
>
> Looks good - although there is a potential problem here with long keywords
> where this does not avoid splitting a single keyword over multiple KW lines
> (as specified in the EMBL specification). This is a corner case though...
OK, not such a rare case:
$ python test_SeqIO_features.py
...
======================================================================
ERROR: test_cor6 (__main__.TestWriteRead)
Write and read back cor6_6.gb
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_SeqIO_features.py", line 1105, in test_cor6
write_read(os.path.join("GenBank", "cor6_6.gb"), "gb")
File "test_SeqIO_features.py", line 35, in write_read
compare_records(gb_records, gb_records2)
File "test_SeqIO_features.py", line 110, in compare_records
if not compare_record(old,new,expect_minor_diffs):
File "test_SeqIO_features.py", line 101, in compare_record
% (key, old.annotations[key], new.annotations[key]))
ValueError: Annotation mis-match for keywords:
['antifreeze protein homology', 'cold-regulated gene', 'cor6.6 gene',
'KIN1 homology']
['antifreeze protein homology', 'cold-regulated gene', 'cor6.6 gene',
'KIN1', 'homology']
----------------------------------------------------------------------
I'll fix this later today...
Peter
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