Annotating features with qualifiers

[benweinberg89]

I could be doing something wrong, but adding qualifiers in dc.biotools.record_operations.annotate_record don't seem to be working for me. Rather the qualifiers are just being added to /note. Annotating using the same qualifiers dict in SeqFeature seems to be working fine for me though.

[veghp]

Thanks for reporting this. The issue seems to be how your sequence editor reads the file and displays the features. This works for me:

import dnacauldron as dc
from Bio import SeqRecord, Seq, SeqFeature
record = SeqRecord.SeqRecord(Seq.Seq("AGATCGATCGATGTAGCT"))
dc.biotools.record_operations.annotate_record(record, test=1234, number="test123")

dc.biotools.write_record(record, target="output.gb")

output.gb:

LOCUS       .                         18 bp    DNA              UNK 01-JAN-1980
DEFINITION  .
ACCESSION   <unknown id>
VERSION     <unknown id>
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     misc_feature    1..18
                     /test=1234
                     /number=test123
ORIGIN
        1 agatcgatcg atgtagct
//

As you see the qualifier is correct in the file, but /test is displayed under /note in an editor, SnapGene for example.