[Biopython] SeqIO.parse for imgt

[Peter Cock]

Thank you Chang, James,

Those details are just the kind of thing I was hoping for.
I don't have time to make the IMGT parser changes today,
so have opened an issue for this on the Biopython GitHub:

https://github.com/biopython/biopython/issues/988

Peter

On Fri, Nov 11, 2016 at 5:00 PM, Liu, Chang <cliu32 at wustl.edu> wrote:
> Thank you very much, James!
> Hi, Peter, here you go - thank you in advance for updating the 'imgt' parser. I really appreciate it. Please let me know if I can be of any assistance!
> Chang
>
> -----Original Message-----
> From: James Robinson [mailto:jrobinso at ebi.ac.uk]
> Sent: Friday, November 11, 2016 10:54 AM
> To: Liu, Chang <cliu32 at wustl.edu>
> Cc: p.j.a.cock at googlemail.com
> Subject: Re: [IPD #99553] hla.dat file and biopython, follow up
>
> Hi,
>
> The key changes post 3.16 are the addition of an SV value to the ID line, these additions should make the format more similar to the ENA style.
>
> ID   HLA00001   standard; DNA; HUM; 3503 BP.
>
> becomes
>
> ID   HLA00001; SV 1; standard; DNA; HUM; 3503 BP.
>
> We have also added the SV value as a line in the file;
>
> SV   HLA00001.1
>
> this is added between the AC and DT lines.
>
> The other change, is the removal of a third DT line, we previously had 3 lines, but have reduced this to two;
>
> DT   01-AUG-1989 (Rel. 1.0.0, Created, Version 1)
> DT   16-DEC-1998 (Rel. 1.0.0, Sequence Updated, Version 1)
> DT   14-APR-2014 (Rel. 3.16.0, Current Release, Version 1)
>
> becomes
>
> DT   01-AUG-1989 (Rel. 1.0.0, Created, Version 1)
> DT   14-OCT-2016 (Rel. 3.26.0, Last Updated, Version 1)
>
> In addition the text within the CC lines has changed from;
>
> CC   --------------------------------------------------------------------------
> CC   Copyrighted by the IMGT/HLA Database, Distributed under the Creative
> CC   Commons Attribution-NoDerivs License, see;
> CC   http://www.ebi.ac.uk/imgt/hla/licence.html for further details.
> CC   --------------------------------------------------------------------------
>
> to
>
> CC   --------------------------------------------------------------------------
> CC   IPD-IMGT/HLA Release Version 3.26.0
> CC   --------------------------------------------------------------------------
> CC   Copyrighted by the IPD-IMGT/HLA Database, Distributed under the Creative
> CC   Commons Attribution-NoDerivs License, see;
> CC   http://www.ebi.ac.uk/ipd/imgt/hla/licence.html for further details.
> CC   --------------------------------------------------------------------------
>
> Thanks
>
> James