[Debian-med-packaging] Bug#792510: blast_formatter: need internet access even if run locally

[Aaron M. Ucko]

> Is there any way to by-pass this ? Telling blast to write sequence in
> the ASN file systematically ? Is it a expected behaviour ?

AFAICT, blastx and the like have no such option at present, but I expect
it would be relatively straightforward to implement one.  Also, it might
be possible to run blast_formatter with environment settings telling it
to retrieve sequence data from your local BLAST database; I'm not sure
what the precise syntax would be, but will investigate and get back to
you.

Meanwhile, I suppose you could work around the issue by disguising the
well-known sequence IDs prior to running makeblastdb:

  sed -e '/^>/y,|,!,; s/^>\([a-z]\)/>lcl|\1' foo.aa > foo-disguised.aa

Of course, you'd then likely want a compensatory transformation on the
output side.

Thanks for all your help diagnosing the problem!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu