Basically, there were two weird features in the JCVI-Syn3a genome:
CDS 3207..4007
/gene="ksgA"
/locus_tag="JCVISYN3A_0004"
/inference="EXISTENCE: similar to AA
sequence:RefSeq:WP_011166215.1"
/codon_start=1
/transl_table=4
/product="16S rRNA
(adenine(1518)-N(6)/adenine(1519)-N(6))-
dimethyltransferase"
/protein_id="AVX54572.1"
/translation="MKAKKYYGQNFISDLNLINKIVDVLDQNKDQLIIEIGPGKGALT
KELVKRFDKVVVIEIDKDMVEILKTKFNHSNLEIIQADVLEIDLKQLISKYDYKNISI
ISNTPYYITSEILFKTLQISDLLTKAVFMLQKEVALRICSNKNENNYNNLSIACQFYS
QRNFEFVVNKKMFYPIPKVDSAIISLTFNDIYKKQVNNDKKFIDFVRLLFNNKRKTIL
NNLNNIIQNKNKALEYLNTLNISSNLRPEQLDIDQYIKLFNLIYNSNF"
The product line (adenine(1518)-N(6)/adenine(1519)-N(6))- messed up because it had an internal /, which we were not checking for. Additionally, there are genes like:
CDS complement(44397..45011)
/locus_tag="JCVISYN3A_0051"
/inference="EXISTENCE: similar to AA
sequence:RefSeq:WP_017698191.1"
/pseudo
/codon_start=1
/transl_table=4
that messed up because we assumed all qualifiers would have a = associated with them. Turns out, assumption false!
Fixes #303
Basically, there were two weird features in the JCVI-Syn3a genome:
The product line
(adenine(1518)-N(6)/adenine(1519)-N(6))-
messed up because it had an internal/
, which we were not checking for. Additionally, there are genes like:that messed up because we assumed all qualifiers would have a
=
associated with them. Turns out, assumption false!