[Debian-med-packaging] Bug#824048: Any change in blastp? (Was: Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1)

[Andreas Tille]

Hi Peter

On Thu, May 19, 2016 at 12:32:17PM +0100, Peter Cock wrote:
> Thanks Andreas,

Thanks for your very quick response.
 
> Ah, https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048
> 
> It looks like yet another minor change to the plain text human
> readable output with the latest NCBI BLAST+ v2.3.0 release is to
> blame,
> 
> $ ~/ncbi_blast/2.2.31+/blastp -query Fasta/rose.pro -evalue 1 -subject
> GenBank/NC_005816.faa | grep "Query= "
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> $ ~/ncbi_blast/2.3.0+/blastp -query Fasta/rose.pro -evalue 1 -subject
> GenBank/NC_005816.faa | grep "Query= "
> Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
> 
> The Biopython test was expecting 10 lines with this pattern, but there
> is now only 1. This may or may not break the parser - I've not yet
> checked:
> 
> https://github.com/biopython/biopython/issues/827

This sounds like a very probable explanation for the effect.  It would
be great if you could come up with a patch (or a new release) so I could
update the Debian package.
 
Thanks a lot for the perfect cooperation

      Andreas.

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