[Biopython-dev] LocationParserError

[Matthias Bernt]

Just in case you need more test cases. I send all cases I found (all
in mitochondria).

NC_016406
join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)

NC_016402
join(complement(NC_016406.1:149815..150200),complement(NC_016406.1:293787..295573),6618..6676,NC_016406.1:181647..181905)

NC_016348
join(complement(NC_016362.1:36881..37266),86404..88057,complement(NC_016391.1:55668..55726),complement(NC_016355.1:144070..144328))

NC_016352
join(NC_016397.1:85333..87643,23246..23267,NC_016390.1:38484..40058)

NC_016355
join(complement(NC_016362.1:36881..37266),NC_016348.1:86404..88057,complement(NC_016391.1:55668..55726),complement(144070..144328))

NC_016358
join(NC_016382.1:95989..97509,31194..34899)

NC_016362
join(complement(36881..37266),NC_016348.1:86404..88057,complement(NC_016391.1:55668..55726),complement(NC_016355.1:144070..144328))

NC_016382
join(95989..97509,NC_016358.1:31194..34899)

NC_016390
join(NC_016397.1:85333..87643,NC_016352.1:23246..23267,38484..40058)

NC_016391
join(complement(NC_016362.1:36881..37266),NC_016348.1:86404..88057,complement(55668..55726),complement(NC_016355.1:144070..144328))

NC_016397
join(85333..87643,NC_016352.1:23246..23267,NC_016390.1:38484..40058)

Matthias

2012/3/9 Peter Cock <p.j.a.cock at googlemail.com>:
> On Fri, Mar 9, 2012 at 7:53 AM, Matthias Bernt <MatatTHC at gmx.de> wrote:
>> Hi,
>>
>> I just got the new RefSeq 52 release and found a really strange error
>> causing an exception:
>>
>> Bio.GenBank.LocationParserError: join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)
>>
>> the accession is: NC_016406. Any ideas?
>>
>> Matthias
>
> That is the most complicated trans_splicing feature I've seen in a while :)
>
> It says gene nad1 is (trans) spliced from four bits, three from the Silene
> vulgarise mitochondria chr1 (i.e. NC_016406.1) from both strands, and
> one from mitochondria chr3 (NC_016402.1). Just in case there was any
> confusion, the human readable note confirms this - not the CDS feature
> has a join of five parts, while the gene has a join of just four - there is
> an intron too.
>
> Looks like a bug in our parser...
>
> Peter