[Biopython] error in records

[Liam Thompson]

Aaaargh. Thanks Peter.

Regards
Liam


On Wed, Oct 20, 2010 at 4:44 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Wed, Oct 20, 2010 at 3:08 PM, Liam Thompson <dejmail at gmail.com> wrote:
> > Hi Peter
> >
> > Thanks for looking at it. I upgraded to biopy 1.55, from 1.54 and it made
> no
> > difference. There is still something funky going on. I have attached the
> > records in the zip textfile, they are the last 2 listed in the file.
> >
> > Thanks
> > Liam
>
> Hi Liam,
>
> I got the zipped GenBank file, thanks. The two problem records
> have been changed - at least, they don't match what I download
> from the NCBI today.
>
> Running the example here the error message from X85254,
>
> Bio.GenBank.LocationParserError: /join(1816..1899,1903..2454)
>
> Hopefully you will agree that this is a much more helpful error
> message than you had before. Looking at the file,
>
> ...
>     gene            /join(1816..1899,1903..2454)
>                     /gene="precore-core"
>     CDS             /join(1816..1899,1903..2454)
>                     /gene="precore-core"
>                     /codon_start=1
> ...
>
> You shouldn't have the leading slash on the join location
> (two cases, gene and CDS entry too).
>
> After fixing that by hand there is an error in X65259.1,
>
> ValueError: Sequence line mal-formed, '       1 AACTCCACAA CCTTCCACCA
> AACTCTGCAA GATCCCAGAG TGAGAGGCCT GTATTTCCCT'
>
> You need another space at the start of that line.
>
> With those three fixes (removing two slashes, adding one space)
> then it seems to parse fine.
>
> Peter
>